The interaction between protoporphyrin molecules (donor) and Si nanocrystals (acceptor) up to 2.5 nm for varying distances and orientations is studied by DFT, semi-empirical and TDDFT methods. Simulations show an effect on electronic structure, indicative of electron charge transfer in parallel orientation and small distances and nonelectron energy transfer for different orientations and larger distances. An absorption-emission spectral overlap is observed. The calculations of coupling and energy transfer rates show a distance dependence typical of fluorescence resonance energy transfer (FRET) in the long range, while in the short and ultra-short range the distance dependence indicates electron transfer in addition to FRET. The Si NCs with the smallest size yield larger couplings than the larger nanocrystals. The PPIX/Si NC coupling was enhanced by adding a plasmon nanoparticle as a bridge in the donor-acceptor system. Results using Au nanoparticles show increased energy transfer rates up to 104 and lower distance dependence.

A combined method of the Dirac-Hartree-Fock (DHF) method and the reference interaction-site model (RISM) theory is reported; this is the initial implementation of the coupling of the four-component relativistic electronic structure theory and an integral equation theory of molecular liquids. In the method, the DHF and RISM equations are solved self-consistently, and therefore the electronic structure of the solute, including relativistic effects, and the solvation structure are determined simultaneously. The formulation is constructed based on the variational principle with respect to the Helmholtz energy, and analytic free energy gradients are also derived using the variational property. The method is applied to the iodine ion (I- ), methyl iodide (CH3 I), and hydrogen chalcogenide (H2 X, where X = O-Po) in aqueous solutions, and the electronic structures of the solutes, as well as the solvation free energies and their component analysis, solvent distributions, and solute-solvent interactions, are discussed.

Algorithms that automatically explore the chemical space have been limited to chemical systems with a low number of atoms due to expensive involved quantum calculations and the large amount of possible reaction pathways. The method described here presents a novel solution to the problem of chemical exploration by generating reaction networks with heuristics based on chemical theory. First, a second version of the reaction network is determined through molecular graph transformations acting upon functional groups of the reacting. Only transformations that break two chemical bonds and form two new ones are considered, leading to a significant performance enhancement compared to previously presented algorithm. Second, energy barriers for this reaction network are estimated through quantum chemical calculations by a growing string method, which can also identify non-octet species missed during the previous step and further define the reaction network. The proposed algorithm has been successfully applied to five different chemical reactions, in all cases identifying the most important reaction pathways.

The hydrogen evolution effect of ZrS2 carrier loaded with transition metal single-atom (SA) was explored by first-principles method. ZrS2 was constructed with transition metal single-atom and dual-atom. The structure-activity relationship of supported single-atom catalysts was described by electronic properties and hydrogen evolution kinetics. The results show that the ZrS2 carrier-loaded atomic-level catalysts are more likely to occur in acidic environments, where the Mo SA load has a higher hydrogen precipitation capacity than the Pt SA. In the case of dual-atom adsorption, most of the hydrogen reduction processes are higher than that of single atom loading, which indicates that the outer orbital hybridization is more likely to lead to the interfacial charge recombination of the catalyst. Thereinto, Ni/Pt @ZrS2 has the lowest Gibbs free energy (0.08 eV), and the synergistic effect of transition metals induces the deviation of the center of the d-band from the Fermi level and improves the dissociation ability of H ions. The design provides a new catalytic model for the HER and provides some ideas for understanding the two-site catalysis.

The factors/structural features which are responsible for the binding, activation and reduction of N2 to NH3 by FeMoco of nitrogenase have not been completely understood well. Several relevant model complexes by Holland et al. and Peters et al. have been synthesized, characterized and studied by theoretical calculations. For a matter of fact, those complexes are much different than real active N2 -binding Fe-sites of FeMoco, which possesses a central C(4-) ion having an eight valence electrons as an μ6 -bridge. Here, a series of [(S3 C(0))Fe(II/I/0)-N2 ]n- complexes in different charged/spin states containing a coordinated σ- and π-donor C(0)-atom which possesses eight outer shell electrons [carbone, (Ph3 P)2 C(0); Ph3 P→C(0)←PPh3 ] and three S-donor sites (i.e. - S-Ar), have been studied by DFT, QTAIM, and EDA-NOCV calculations. The effect of the weak field ligand on Fe-centres and the subsequent N2 -binding has been studied by EDA-NOCV analysis. The role of the oxidation state of Fe and N2 -binding in different charged and spin states of the complex have been investigated by EDA-NOCV analyses. The intrinsic interaction energies of the Fe-N2 bond are in the range from -42/-35 to -67 kcal/mol in their corresponding ground states. The S3 C(0) donor set is argued here to be closer to the actual coordination environment of one of the six Fe-centres of nitrogenase. In comparison, the captivating model complexes reported by Holland et al. and Peter et al. possess a stronger π-acceptor C-ring (S2 Cring donor, π-C donor) and stronger donor set like CP3 (σ-C donor) ligands, respectively.

Polymorphic beryllium oxide has been theoretically investigated from first principles as regards orbital occupancies, chemical bonding, polarization, as well as dielectric properties. By means of Crystal-Orbital Bond Index (COBI) analysis, the important role of the 2p orbitals on beryllium has been elucidated, in particular in terms of the correlation between polarization and beryllium-atom displacement, including the impact of the latter on the covalency of the BeO bond. In addition, several structural possibilities for a Bex Mg1-x O solid solution have been investigated for a Be content between 6% and 22%; for those, dynamically stable structures have been found, displaying large polarization values, more covalent BeO bonds, and a tendency for tetrahedral Be coordination. The dynamically unstable structures, however, resemble rock-salt BeO in their local structural properties around the Be atom. High dielectric constants and band gaps indicating insulating behavior have been found for those.

Although cyclic voltammetry (CV) measurements in solution have been widely used to determine the highest occupied molecular orbital energy (EHOMO ) of semiconducting organic molecules, an understanding of the experimentally observed discrepancies due to the solvent used is lacking. To explain these differences, we investigate the solvent effects on EHOMO by combining density functional theory and molecular dynamics calculations for four donor molecules with a common backbone moiety. We compare the experimental EHOMO values to the calculated values obtained from either implicit or first solvation shell theories. We find that the first solvation shell method can capture the EHOMO variation arising from the functional groups in solution, unlike the implicit method. We further applied the first solvation shell method to other semiconducting organic molecules measured in solutions for different solvents. We find that the EHOMO obtained using an implicit method is insensitive to solvent choice. The first solvation shell, however, produces EHOMO values that are sensitive to solvent choices and agrees with published experimental results. The solvent sensitivity arises from a hierarchy of three effects: (1) the solute electronic state within a surrounding dielectric continuum, (2) ambient temperature or solvent atoms changing the solute geometry, and (3) electronic interactions between the solute and solvents. The implicit method, on the other hand, only captures the effect of a dielectric environment. Our findings suggest that EHOMO obtained by CV measurements should account for the influence of solvent when the results are reported, interpreted, or compared to other molecules.

This review aims to be a comprehensive, authoritative, critical, and accessible review of general interest to the chemistry community; because the electrophilicity index is a very useful global reactivity descriptor defined within a conceptual density functional theory framework. Our group has also introduced electrophilicity based new global and local reactivity descriptors and also new associated electronic structure principles, which are important indicators of structure, stability, bonding, reactivity, interactions, and dynamics in a wide variety of physico-chemical systems and processes. This index along with its local counterpart augmented by the associated electronic structure principles could properly explain molecular vibrations, internal rotations and various types of chemical reactions. The concept of the electrophilicity index has been extended to dynamical processes, excited states, confined environment, spin-dependent and temperature-dependent situations, biological activity, site selectivity, aromaticity, charge removal and acceptance, presence of external perturbation through solvents, external electric and magnetic fields, and so forth. Although electrophilicity and its local variant can adequately interpret the behavior of a wide variety of systems and different physico-chemical processes involving them, their predictive potential remains to be explored. An exhaustive review on all these aspects will set the tone of the future research in that direction.

The bonding situation in the tricoordinated beryllium phenyl complexes [BePh3 ]- , [(pyridine)BePh2 ] and [(trimethylsilyl-N-heterocyclic imine)BePh2 ] is investigated experimentally and computationally. Comparison of the NMR spectroscopic properties of these complexes and of their structural parameters, which were determined by single crystal X-ray diffraction experiments, indicates the presence of π-interactions. Topology analysis of the electron density reveals elliptical electron density distributions at the bond critical points and the double bond character of the beryllium-element bonds is verified by energy decomposition analysis with the combination of natural orbital for chemical valence. The present beryllium-element bonds are highly polarized and the ligands around the central atom have a strong influence on the degree of π-delocalization. These results are compared to related triarylboranes.

In this paper, the SHARK integral generation and digestion engine is described. In essence, SHARK is based on a reformulation of the popular McMurchie/Davidson approach to molecular integrals. This reformulation leads to an efficient algorithm that is driven by BLAS level 3 operations. The algorithm is particularly efficient for high angular momentum basis functions (up to L = 7 is available by default, but the algorithm is programmed for arbitrary angular momenta). SHARK features a significant number of specific programming constructs that are designed to greatly simplify the workflow in quantum chemical program development and avoid undesirable code duplication to the largest possible extent. SHARK can handle segmented, generally and partially generally contracted basis sets. It can be used to generate a host of one- and two-electron integrals over various kernels including, two-, three-, and four-index repulsion integrals, integrals over Gauge Including Atomic Orbitals (GIAOs), relativistic integrals and integrals featuring a finite nucleus model. SHARK provides routines to evaluate Fock like matrices, generate integral transformations and related tasks. SHARK is the essential engine inside the ORCA package that drives essentially all tasks that are related to integrals over basis functions in version ORCA 5.0 and higher. Since the core of SHARK is based on low-level basic linear algebra (BLAS) operations, it is expected to not only perform well on present day but also on future hardware provided that the hardware manufacturer provides a properly optimized BLAS library for matrix and vector operations. Representative timings and comparisons to the Libint library used by ORCA are reported for Intel i9 and Apple M1 max processors.

Stabilization of hydrogen-substituted group 13-15 compounds H2 EE'H2 (E = B, Al, Ga; E' = P, As, Sb) by Lewis acids is considered at B3LYP/def2-TZVP, B3LYP-D3/def2-TZVP and M06-2X/def2-TZVP levels of theory. It is shown, that for many Lewis acids additional reactivity beyond the DA complex formation with H2 EE'H2 monomer is expected. In case of complexation with E(C6 F5 )3 , F/H exchange reactions with group 13 bound hydrides are predicted to be exothermic and accompanied by the activation energies which are smaller than dissociation of the complex into components. In case of complex formation with transition metal (TM) carbonyls, additional O → Al, TM-C → Al interactions are observed, which in several cases lead to cyclic structures. The most promising candidates for the experimental studies have been identified. Synthetic approaches to the most promising LA-only stabilized compounds are recommended.

ESE-EE (Easy Solvation Estimation with Electronegativity equalization) is a quick method for estimation of solvation-free energies ΔGºsolv , which uses a thoroughly fitted electronegativity equalization (EE) scheme to obtain atomic charges, which are further employed in a scaled noniterative COSMO-like calculation to evaluate the electrostatic component of ΔGºsolv . Nonelectrostatic corrections including adjustable parameters are also added. For neutral solutes, ESE-EE yields a mean absolute error (MAE) in ΔGsolv ° of 1.5 kcal/mol for aqueous solutions; 1.0 kcal/mol for nonaqueous polar protic solvents; 0.9 kcal/mol for polar aprotic solvents; and about 0.6 kcal/mol for nonpolar solvents. Since ESE-EE only requires a molecular geometry as input for a ΔGºsolv prediction, it can be utilized for a rapid screening of ΔGºsolv for large neutral molecules. However, for ionic solutes, ESE-EE yields larger errors (typically several kcal/mol) and is recommendable for preliminary estimations only. Upon a special refitting, ESE-EE is able to yield partition coefficients with a good accuracy.

The necessity of the recent incorporation of new external variables in the context of conceptual DFT (CDFT) is discussed based on the ever-increasing portfolio of experimental reaction conditions in the endeavor of experimentalists to synthesize new molecules with unprecedented properties. Electric and magnetic fields (ε and B), mechanical forces (F), and confinement are proposed as valuable new variables, extending conventional CDFT and its associated response functions. A finite field approach is used to calculate the evolution of both global and local descriptors in a selected series of atomic and molecular applications, and from it derive new response function involving, with one exception, the first derivative to the field considered. The electric field results, displaying, for example, a case of a field-induced enantioselectivity in the Fukui function, may be instrumental in the recent upsurge of chemistry in oriented external electric fields. The study of atomic electronegativity and hardness in magnetic fields displays a piecewise behavior, associated to configurational jumps upon increasing field strength and reveals an overall compression of their ranges for stronger fields, which may be guiding upon investigating chemistry in extremely high fields like in white dwarfs. The evolution of the electronegativity and hardness of diatomics under mechanical force can elegantly be traced back to differences in their equilibrium distance in the neutral, cationic, and anionic state. The well-known reduction of the polarizability under confinement can be seen as a fore-runner of the increasing hardness of atoms under pressure, presently under investigation. Periodicity showing up in a spontaneous way in the variety of properties is a leitmotiv in this study, as well as the interconnections/analogies between the different response functions.

To improve the catalytic activity of 3d transition metal catalysts, redox-active ligands are a promising tool. These ligands influence the oxidation state of the metal center as well as the ground spin-state and make the experimental determination of both properties challenging. Therefore, first-principles calculations, in particular employing density functional theory with a proper choice of exchange-correlation (xc) functional, are crucial. Common xc functionals were tested on a simple class of metal complexes: homoleptic, octahedral tris(diimine) iron(II) complexes. The spin-state energy splittings for most of these complexes showed the expected linear dependence on the amount of exact exchange included in the xc functionals. Even though varying redox-activity affects the electronic structure of the complexes considerably, the sensitivity of the spin-state energetics to the exact exchange admixture is surprisingly small. For iron(II) complexes with highly redox-active ligands and for a broad range of ligands in the reduced tris(diimine) iron(I) complexes, self-consistent field convergence to local minima was observed, which differ from the global minimum in the redox state of the ligand. This may also result in convergence to a molecular structure that corresponds to an energetically higher-lying local minimum. One criterion to detect such behavior is a change in the sign of the slope for the dependence of the spin-state energy splittings on the amount of exact exchange. We discuss possible protocols for dealing with such artifacts in cases in which a large number of calculations makes checking by hand unfeasible.

The classic pnictogen dichotomy stands for the great contrast between triply bonding very stable N2 molecules and its heavier congeners, which appear as dimers or oligomers. A banner example involves phosphorus as it occurs in nature as P4 instead of P2 , given its weak π-bonds or strong σ-bonds. The P2 synthetic value has brought Lewis bases and metal coordination stabilization strategies. Herein, we discuss the unrealized encapsulation alternative using the well-known fullerenes' capability to form endohedral and stabilize otherwise unstable molecules. We chose the most stable fullerene structures from Cn (n = 50, 60, 70, 80) and experimentally relevant from Cn (n = 90 and 100) to computationally study the thermodynamics and the geometrical consequences of encapsulating P2 inside the fullerene cages. Given the size differences between P2 and P4 , we show that the fullerenes C70 -C100 are suitable cages to side exclude P4 and host only one molecule of P2 with an intact triple bond. The thermodynamic analysis indicates that the process is favorable, overcoming the dimerization energy. Additionally, we have evaluated the host-guest interaction to explain the origins of their stability using energy decomposition analysis.

The (C60 CN)- formed by the reaction of CN- with fullerene shows high electron rich character, very similar to C60 ˙- , and it behaves as a large anion. Similar to Cp- , the bulky anion, (C60 CN)- , acts as a strong η5 ligand towards transition metal centers. Previous studies on η5 coordination of fullerene cage are reported for pseudo fullerenes whereas the present study deals with sandwich complexes of (C60 CN)- with Fe(II), Ru(II), Cr(II), Mo(II), and Ni(II) and multi-decker sandwich complexes of CN-fullerides with Fe(II). The structural parameters of these complexes and the corresponding Cp- complexes showed very close resemblance. Analysis of the metal-to-carbon bonding molecular orbitals showed that sandwich complex [Fe(η5 -(C60 CN)- )2 ] exhibit bonding features very similar to that of ferrocene. Also, a 6-fold decrease in the band gap energy is observed for [Fe(η5 -(C60 CN)- )2 ] compared to ferrocene. The energy of dissociation (ΔE) of the ligand (C60 CN)- from [Fe(η5 -(C60 CN)- )2 ] is slightly lower than the ΔE of a Cp* ligand from a ferrocene derivative wherein each cyclopentadienyl unit is substituted with four tertiary butyl groups. The (C60 CN)- ligand behaved as one of the bulkiest ligands in the chemistry of sandwich complexes. Further, the coordinating ability of the dianion, (C60 (CN)2 )2- is evaluated which showed strong coordination ability simultaneously with two metal centers leading to the formation of multi-decker sandwich and pearl-necklace type polymeric structures.

The development of ligands capable of effectively stabilizing highly reactive main-group species has led to the experimental realization of a variety of systems with fascinating properties. In this work, we computationally investigate the electronic, structural, energetic, and bonding features of proximity-enforced group 13-15 homodimers stabilized by a rigid expanded pincer ligand based on the 1,8-naphthyridine (napy) core. We show that the redox-active naphthyridine diimine (NDI) ligand enables a wide variety of structural motifs and element-element interaction modes, the latter ranging from isolated, element-centered lone pairs (e.g., E = Si, Ge) to cases where through-space π bonds (E = Pb), element-element multiple bonds (E = P, As) and biradical ground states (E = N) are observed. Our results hint at the feasibility of NDI-E2 species as viable synthetic targets, highlighting the versatility and potential applications of napy-based ligands in main-group chemistry.

Today's demand for precisely predicting chemical reactions from first principles requires research to go beyond Gibbs' free energy diagrams and consider other effects such as concentrations and quantum tunneling. The present work introduces overreact, a novel Python package for propagating chemical reactions over time using data from computational chemistry only. The overreact code infers all differential equations and parameters from a simple input that consists of a set of chemical equations and quantum chemistry package outputs for each chemical species. We evaluate some applications from the literature: gas-phase eclipsed-staggered isomerization of ethane, gas-phase umbrella inversion of ammonia, gas-phase degradation of methane by chlorine radical, and three solvation-phase reactions. Furthermore, we comment on a simple solvation-phase acid-base equilibrium. We show how it is possible to achieve reaction profiles and information matching experiments.

Traditional π-covalent interactions have been proved in the non-metal halogen bond adducts formed by chloride and halogenated triphenylamine-based radical cations. In this study, we have rationally designed two metal-involving halogen bond adducts with π-covalency property, such as [L1-Pd···I-PTZ]+ (i.e., 1) and [L2-Pd···I-PTZ]+ (i.e., 2), in which the square-planar palladium complexes serve as halogen bond acceptor and 3,7-diiodo-10H-phenothiazine radical cation (i.e., [I-PTZ]•+ ) acts as halogen bond donor. Noncovalent interaction analysis and quantum theory of atoms in molecules analysis revealed that there are notable halogen bond interactions along the Pd···I direction without genuine chemical bond formed in both designed adducts. Energy decomposition analysis together with natural orbital for chemical valence calculations were performed to gain insight into their bonding nature, which demonstrated the presence of remarkable π-covalent interactions and σ-covalent interactions in both 1 and 2. We therefore proposed a new strategy for building the metal-involving halogen bonds with π-covalency property, which will help the further development of new types of halogen bonds.

N-heterocyclic carbenes (NHCs) have been established to be effective organocatalysts for facilitating the benzoin condensation and many other reactions. These reactions involve the formation of a Breslow intermediate (BI), which exhibits umpolung chemistry. To facilitate organocatalysis, several new cyclic carbenes are being introduced, four-membered NHCs are of special interest. Whether these NHCs can exhibit catalytic influence or not, can be evaluated by exploring the potential energy surface (PES) of the benzoin condensation reaction. Quantum chemical analysis has been carried out to compare the PES of these four-membered NHCs with that of standard five-membered NHCs to explore their catalytic ability. The barrier for the first step of the reaction for the formation of BI is comparable in all the cases. But the barrier for the second step of the reaction leading to the benzoin formation from BI is estimated to be very high for the four membered NHCs. These results indicate that the probability of identifying and isolating the BI is very high in comparison to the completion of benzoin condensation reaction in the case of the four-membered NHCs.

In the current study, the coordination chemistry of nine-coordinate Ac(III) complexes with 35 monodentate and bidentate ligands was investigated using density functional theory (DFT) in terms of their geometries, charges, reaction energies, and bonding interactions. The energy decomposition analysis with naturals orbitals for chemical valence (EDA-NOCV) and the quantum theory of atoms in molecules (QTAIM) were employed as analysis methods. Trivalent Ac exhibits the highest affinities toward hard acids (such as charged oxophilic donors, fluoride), so its classification as a hard acid is justified. Natural population analysis quantified the involvement of 5f orbitals on Ac to be about 30% of total valence electron natural configuration indicating that Ac is a member of the actinide series. Pearson correlation coefficients were used to study the pairwise correlations among the bond lengths, ΔG reaction energies, charges on Ac and donor atoms, and data from EDA-NOCV and QTAIM. Strong correlations and anticorrelations were found between Voronoi charges on donor atoms with ΔG, EDA-NOCV interaction energies and QTAIM bond critical point densities.

Aminoborane, H2 NBH2 and its isotopologues, H2 N10 BH2 , D2 NBD2 , and D2 N10 BD2 , have been studied by high-level ab initio methods. All calculations rely on multidimensional potential energy surfaces and dipole moment surfaces including high-order mode coupling terms, which have been obtained from electronic structure calculations at the level of explicitly correlated coupled-cluster theory, CCSD(T)-F12, or the distinguishable cluster approximation, DCSD. Subsequent vibrational structure calculations based on second-order vibrational perturbation theory, VPT2, and vibrational configuration interaction theory, VCI, were used to determine rotational constants, centrifugal distortion constants, vibrationally averaged geometrical parameters and (an)harmonic vibrational frequencies. The impact of core-correlation effects is discussed in detail. Rovibrational VCI calculations were used to simulate the gas phase spectra of these species and an in-depth analysis of the ν7 band of aminoborane is provided. Color-coding is used to reveal the identity of the individual progressions of the rovibrational transitions for this particular mode.

The metal dinitrogen bonding in a wide series of terminal end-on dinitrogen complexes is investigated with the charge displacement analysis based on natural orbitals of chemical valence (CD-NOCV). The effect of the σ donation and π backdonation on the NN bond are discussed and compared with the observations for a series of carbonyl complexes, published in 2016 by Tarantelli et al. The σ donation is relative invariant over the series of dinitrogen complexes and has no significant effect on the NN bond strength, whereas the π backdonation causes a considerable elongation of the NN bond. Some uncommon examples of weakly bound dinitrogen with blue-shifted stretching frequency compared to free N2 (ν = 2330 cm-1 ) are known. The dinitrogen bonding in these complexes is simulated with a point charge. Apparently, electrostatics account for the shortened N─N bond in these systems.

Quantum computers are special purpose machines that are expected to be particularly useful in simulating strongly correlated chemical systems. The quantum computer excels at treating a moderate number of orbitals within an active space in a fully quantum mechanical manner. We present a quantum phase estimation calculation on F2 in a (2,2) active space on Rigetti's Aspen-11 QPU. While this is a promising start, it also underlines the need for carefully selecting the orbital spaces treated by the quantum computer. In this work, a scheme for selecting such an active space automatically is described and simulated results obtained using both the quantum phase estimation (QPE) and variational quantum eigensolver (VQE) algorithms are presented and combined with a subtractive method to enable accurate description of the environment. The active occupied space is selected from orbitals localized on the chemically relevant fragment of the molecule, while the corresponding virtual space is chosen based on the magnitude of interactions with the occupied space calculated from perturbation theory. This protocol is then applied to two chemical systems of pharmaceutical relevance: the enzyme [Fe] hydrogenase and the photosenzitizer temoporfin. While the sizes of the active spaces currently amenable to a quantum computational treatment are not enough to demonstrate quantum advantage, the procedure outlined here is applicable to any active space size, including those that are outside the reach of classical computation.

Closo-carborane anions are prominent, whereas the cations of the same are less abundant in the literature. As these ions have similar size and are weakly coordinating, the ionic liquids of these two ions could have important applications in many areas of chemistry. In view of limited number of polyhedral carborane cations available, we revisited the rearrangement of dicarboranyl methyl cation (7-CH2 7,9-nido-C2 B9 H10 + ) using ab initio molecular dynamics calculations with metadynamics. Our simulations confirmed the concerted mechanism of the rearrangement. We believe this work will resume the interest in its synthesis and carborane cations in general.

Many binuclear nickel complexes have NiNi distances suggesting NiNi covalent bonds, including lantern-type complexes with bridging bidentate ligands. This DFT study treats tetragonal, trigonal, and digonal lantern-type complexes with the formamidinate, guanidinate, and formate ligands, besides some others. Formal bond orders (ranging from zero to two) are assigned to all the NiNi bonds on the basis of MO occupancy considerations. A VB-based electron counting approach assigns plausible resonance structures to the dinickel cores. Model tetragonal complexes with the dimethylformamidinate and the dithioformate ligands have singlet ground states whose non-covalently bonded NiNi distances are close to those in their experimentally known counterparts. Trigonal dinickel complexes are unknown, but are predicted to have quartet ground states with NiNi bonds of order 0.5. The model digonal complexes are predicted to have triplet ground states, but the predicted NiNi bond lengths are longer than those found in their experimentally known counterparts. This could owe to inadequate treatment of electron correlation by DFT in these short NiNi bonds with their multiconfigurational character. All the NiNi bond distances here are categorized into ranges according to the NiNi bond orders of 0, 0.5, 1, 1.5, and 2, no NiNi bonds of order higher than two being identified. The NiNi bonds of given order in these lantern-type complexes are consistently shorter than the corresponding NiNi bonds in dinickel complexes having carbonyl ligands, attributable to the metalmetal bond lengthening effect of CO ligands.

Recently fabricated 2D biphenylene network is an astonishing solid-state material, which possesses unique metal-like conductive properties. At the same time, two-dimensional boron nitride network (2D-BN)-an isoelectronic and structural analogue of biphenylene network, is an insulator with a wide direct bandgap. This study investigates the relationship between the electronic properties and chemical bonding patterns for these species. It is shown that the insulating 2D-BN network possesses a strong localization of electron density on the nitrogen atoms. In turn, for a carbon-containing sheet, we found a highly delocalized electron density and an appreciable overlap of pz orbitals of neighboring C6 rings, which might be a reason for the conductive properties of the material.

The bonding and reactivity of the hypo-coordinated compounds with one, two, and four non-bonding electrons namely, carbon-centered free radical, carbenes, and carbones were well earlier established. Here, we report stability, bonding and reactivity of compounds RCL, where R is one-electron donor group (R = CH3 (a), CHO (b), and NO2 (c)) and L is two-electron donor ligand (L = cAAC (1), CO (2), NHC (3) and PMe3 (4)), having three non-bonding electrons. The ground states of molecules exist in a doublet with a lone pair of electrons and an unpaired electron at the central carbon atom (C1). The spin hops over from π- to σ-type orbitals is observed as the π-acceptor strength of the donor ligand increases. The replacement of the methyl group by CHO and NO2 indicate that the cAAC and CHO substituted compounds gives a σ-radical except in compound 2c. These molecules show very high proton affinity and exothermic reaction energy for the hydrogen atom addition indicating dual reactivity namely, radical and lone pair reactivity.

Computations play a critical role in deciphering the nature of host-guest interactions both at qualitative and quantitative levels. Reliable quantum chemical computations were employed to assess the nature, binding strength, and selectivity of ionic, and neutral guests with benzenoid hosts. Optimized complex structures reveal that alkali and ammonium ions are found to be in the hydrophobic cavity, while halide ions are outside, while both complexes elicit substantial binding energy. The origin of the selectivity of host toward the guest has been traced to the interaction and deformation energies, and the nature of associated interactions is quantified using energy decomposition and the Quantum Theory of Atoms in Molecules analyses. While the larger hosts lead to loosely bound complexes, as assessed by the longer intermolecular distances, the binding strengths are proportional to the size of the host systems. The binding of cationic complexes is electrostatic or polarization driven while exchange term dominates the anionic complexes. In contrast, dispersion contribution is a key in neutral complexes and plays a pivotal role in stabilizing the polyatomic complexes.

Low-energy spectra of single-molecule magnets (SMMs) are often described by Heisenberg Hamiltonians. Within this formalism, exchange interactions between magnetic centers determine the ground-state multiplicity and energy separation between the ground and excited states. In this contribution, we extract exchange coupling constants (J) for a set of iron (III) binuclear and tetranuclear complexes from all-electron calculations using non-collinear spin-flip time-dependent density functional theory (NC-SF-TDDFT). For 12 binuclear complexes with J-values ranging from -6 to -132 cm-1 , our benchmark calculations using the short-range hybrid ωPBEh functional and 6-31G(d,p) basis set agree well with the experimentally derived values (mean absolute error of 4.7 cm-1 ). For the tetranuclear SMMs, the computed J constants are within 6 cm-1 from the experimentally derived values. We explore the range of applicability of the Heisenberg model by analyzing bonding patterns in these Fe(III) complexes using natural orbitals (NO), their occupations, and the number of effectively unpaired electrons. The results illustrate the efficiency of the spin-flip protocol for computing the exchange couplings and the utility of the NO analysis in assessing the validity of effective spin Hamiltonians.

The structural properties of μ2 -bridged porphyrinic double-decker complexes are investigated and the influence of various ligands, metals, substituents, and bridging atoms on the dominant structural motif is elucidated. A variety of quantum chemical methods including semiempirical (SQM) methods and density functional theory (DFT) is assessed for the calculation of ecliptic and staggered conformational energies. Local coupled cluster (DLPNO-CCSD(T1)) data are generated for reference. The r2 SCAN-3c composite scheme as well as the B2PLYP-D4/def2-QZVPP approach are identified as reliable methods. Energy decomposition analyses (EDA) and localized molecular orbital analyses (LMO) are used to investigate the bonding situation and the nature of the inter-ligand interaction energy underlining the crucial role of attractive London dispersion interactions. Targeted modification of the bridging atom, e.g., by replacing O2- by S2- is shown to drastically change the major structural features of the investigated complexes. Further, the influence of different substituents of varying size at the phthalocyanine ligand regarding the dominant conformation is described.

Actinoid tetroxide molecules AnO4 (An = Ac - Cm) are investigated with the ab initio density matrix renormalization group (DMRG) approach. Natural orbital shapes are used to read out the oxidation state (OS) of the f-elements, and the atomic orbital energies and radii are used to explain the trends. The highest OSs reveal a "volcano"-type variation: For An = Ac - Np, the OSs are equal to the number of available valence electrons, that is, AcIII , ThIV , PaV , UVI , and NpVII . Starting with plutonium as the turning point, the highest OSs in the most stable AnO4 isomers then decrease as PuV , AmV , and CmIII , indicating that the 5f-electrons are hard to be fully oxidized off from Pu onward. The variations are related to the actinoid contraction and to the 5f-covalency characteristics. Combined with previous work on OSs, we review their general trends throughout the periodic table, providing fundamental understanding of OS-relevant phenomena.

Perfluorinated cycloparaphenylenes (F-[n]CPP, n = 5-8), boron nitride nanohoop (F-[5]BNNH), and buckybowls (F-BBs) were proposed as anion receptors via anion-π interactions with halide anions (Cl- , Br- and I- ), and remarkable binding strengths up to -294.8 kJ/mol were computationally verified. The energy decomposition approach based on the block-localized wavefunction method, which combines the computational efficiency of molecular orbital theory and the chemical intuition of ab initio valence bond theory, was applied to the above anion-π complexes, in order to elucidate the nature and selectivity of these interactions. The overall attraction is mainly governed by the frozen energy component, in which the electrostatic interaction is included. Remarkable binding strengths with F-[n]CPPs can be attributed to the accumulated anion-π interactions between the anion and each conjugated ring on the hoop, while for F-BBs, additional stability results from the curved frameworks, which distribute electron densities unequally on π-faces. Interestingly, the strongest host was proved to be the F-[5]BNNH, which exhibits the most significant anisotropy of the electrostatic potential surface due to the difference in the electronegativities of nitrogen and boron. The selectivity of each host for anions was explored and the importance of the often-overlooked Pauli exchange repulsion was illustrated. Chloride anion turns out to be the most favorable anion for all receptors, due to the smallest ionic radius and the weakest destabilizing Pauli exchange repulsion.

Herein we show a density functional theory-based study performed on two recently predicted polymorphs of the BeH2 monolayer, α-BeH2 and β-BeH2 . The α-BeH2 phase possesses an in-plane negative Poisson's ratio (NPR), introducing it into the unique group of auxetic materials. Our assessment delves into the linear-elastic and finite-strain regimes to understand both polymorphs' structural and mechanical responses to deformation. We find that the in-plane NPR is shown to be only parallel to the bonds in α-BeH2 and remains along the uniaxial tensile path. Concomitantly, an out-of-plane transition toward auxetic is also revealed in regions exhibiting conventional Poisson's ratios, making α-BeH2 a bidirectionally auxetic material. While phase transitions in β-BeH2 are triggered at very short strains, α-BeH2 displays excellent elasticity against tension, superior to that of most currently known 2D materials.

The reactions of coinage metal atoms Cu, Ag and Au with carbon suboxide (C3 O2 ) are studied by matrix isolation infrared spectroscopy. The weakly bound complexes TM-η1 -C3 O2 (TM=Cu, Ag, Au), in which the carbon suboxide ligand binds to the metal center in the monohapto fashion are formed as initial reaction products. The complexes subsequently isomerize to the inserted products OCTMCCO upon visible light (λ = 400-500 nm) excitation. The analysis of the electronic structure using modern quantum chemistry methods suggests that the linear OCTMCCO complexes are best described by the bonding interactions between the TM+ cation in the electronic singlet ground state and the [OC…CCO]- ligands in the doublet state forming two TM+  ← ligands σ donation and two TM+  → ligands π backdonation bonding components. In addition, the CuCCO, AgCCO and AuCCO complexes are also formed, which are predicted to be bent.

The interaction of ammonia with Ben (n < 1-10) clusters has been investigated by density functional theory and ab initio calculations. The main conclusion is that, regardless of the size of the Be cluster, neither the structure of ammonia nor that of the Be clusters are preserved due to a systematic dissociation of its NH bonds and a spontaneous H-shift toward the available Be atoms. This H migration not only leads to rather stable BeH bonds, but dramatically enhances the strength of the BeN bonds as well. Accordingly, the maximum stability is found for the interaction with the beryllium trimer, leading to a complex with three NBe and three BeH bonds. Another maximum in stability, although lower than that reached for n = 3, is found for the Be heptamer, since from n = 6, a new NBe bond is formed, so that complexes from n = 6 to n = 10 are characterized by the formation of a NBe4 moiety, whose stability reaches a maximum at n = 7. The bonding characteristics of the different species formed are analyzed by means of AIM, NBO, ELF and AdNDP approaches.

Copper guanidine-quinoline complexes are an important class of bioinorganic complexes that find utilization in electron and atom transfer processes. By substitution of functional groups on the quinoline moiety the electron transfer abilities of these complexes can be tuned. In order to explore the full substitution space by simulations, the accurate theoretical description of the effect of functional groups is essential. In this study, we compare three different methods for the theoretical description of the structures. We use the semi-empirical tight-binding method GFN2-xTB, the density functional TPSSh and the double-hybrid functional B2PLYP. We evaluate the methods on five different complex pairs (Cu(I) and Cu(II) complexes), and compare how well calculated energies can predict the redox potentials. We find even though B2PLYP and TPSSh yield better accordance with the experimental structures. GFN2-xTB performs surprisingly well in the geometry optimization at a fraction of the computational cost. TPSSh offers a good compromise between computational cost and accuracy of the redox potential for real-life complexes.

On-surface synthesis has become a thriving topic in surface science. The Ullmann coupling reaction is the most applied synthetic route today, but the nature of the organometallic intermediate is still under discussion. We investigate the bonding nature of prototypical intermediate species (phenyl, naphthyl, anthracenyl, phenanthryl, and triphenylenyl) on the Cu(111) surface with a combination of plane wave and atomic orbital basis set methods using density functional theory calculations with periodic boundary conditions. The surface bonding is shown to be of covalent nature with a polarized shared-electron bond supported by π-back donation effects using energy decomposition analysis for extended systems (pEDA). The bond angle of the intermediates is determined by balancing dispersion attraction and Pauli repulsion between adsorbate and surface. The latter can be significantly reduced by adatoms on the surface. We furthermore investigate how to choose computational parameters for pEDA of organic adsorbates on metal surfaces efficiently and show that bonding interpretation requires consistent choice of the density functional.

This work reports the development and testing of an automated algorithm for estimating the energies of weakly bound molecular clusters employing correlated theory. Firstly, the monomers and dimers of (homo/hetero) clusters are identified, and the sum of one-body and two-body contributions to correlation energy is calculated. The addition of this contribution to the Hartree-Fock full calculation (FC) energies provides a good estimate of the total energies at Møller-Plesset second-order perturbation theory (MP2)/coupled-cluster method with singles and doubles (CCSD) (T)-level theory using augmented Dunning basis sets. The estimated energies for several test clusters show an excellent agreement with their FC counterparts, with a substantial wall-clock time saving employing off-the-shelf hardware. Furthermore, the complete basis set (CBS) limit for MP2 energy computed using the two-body approach also agrees with its CBS energy with its FC counterpart.

Here, the effect of solvent on the stability of non-covalent complexes, was studied. These complexes were from previously published S22, S66, and X40 datasets, which include hydrogen-, halogen- and dispersion-bonded complexes. It was shown that the charge transfer in the complex determines whether the complex is stabilized or destabilized in solvent.

Multi-layer molecular rotors represent a class of unique combination of topology and bonding, featuring a barrier-free rotation of one layer with respect to other layers. This emerging fluxional behavior has been found in a few doped boron clusters. Herein, we strongly enrich this intriguing family followed by an effective design strategy, summarized as essential factors: i) considerable electrostatic interactions originated from a strong charge transfer between layers; ii) the absence of strong covalent bonds between layers; and iii) fully delocalized σ/π electrons from at least one layer. We found that planar hypercoordinate motifs consisting of monocyclic boron rings and metals with σ + π dual aromaticity can be regarded as one promising layer, which can support the suspended X2 (X = Zn, Cd, Hg) dimers. By detailed investigations of thermodynamic and kinetic stabilities of 60 species, eventually, MB7 X2 - and MB8 X2 (X = Zn, Cd; M = Be, Ru, Os; Be works only for Zn-based cases) clusters were verified to be the global-minimum two-layer molecular rotors. Especially, their electronic structure analyses vividly confirm the practicability of the electronic structure requirements mentioned above for designing multi-layer molecular rotors.

A new theoretical method, referred to as Generalized Langevin Mode Analysis (GLMA), is proposed to analyze the mode of structural fluctuations of a biomolecule in solution. The method combines the two theories in the statistical mechanics, or the Generalized Langevin theory and the RISM/3D-RISM theory, to calculate the second derivative, or the Hessian matrix, of the free energy surface of a biomolecule in aqueous solution, which consists of the intramolecular interaction among atoms in the biomolecule and the solvation free energy. The method is applied to calculate the wave-number spectrum of an alanine dipeptide in water for which the optical heterodyne-detected Raman-induced spectroscopy (RIKES) spectrum is available to compare with. The theoretical analysis reproduced the main features of the experimental spectrum with respect to the peak positions of the four bands around ~90 cm-1 , ~240 cm-1 , ~370 cm-1 , and 400 cm-1 , observed in the experimental spectrum, in spite that the physics involved in the two spectrum was not exactly the same: the experimental spectrum includes the contributions from the dipeptide and the water molecules interacting with the solute, while the theoretical one is just concerned with the solute molecule, influenced by solvation. Two major discrepancies between the theoretical and experimental spectra, one in the band intensity around ~100 cm-1 , and the other in the peak positions around ~370 cm-1 , are discussed in terms of the fluctuation mode of water molecules interacting with the dipeptide, which is not taken explicitly into account in the theoretical analysis.

Argon compounds play an important role in the mass spectrometry with inductively coupled plasma and other applications. At the same time, there is a little knowledge of their electronic terms and thermodynamic functions due to the complexity of experimental observations. In this work, the ab initio simulations are performed to obtain the interatomic interaction potentials for the ground and excited states of ArN and ArN+ . Using these potentials, the vibrational-rotational partition functions and thermodynamic properties in the gas phase are calculated for these molecules at the temperature range of 298.15-10,000 K. The errors of the thermodynamic functions associated with the approximation of interatomic interaction potentials are estimated.

The selectivity and the nature of the molecular mechanism of the [3 + 2] cycloaddition (32CA) reaction between 2-(dimethylamino)-1H-indene-1,3(2H)-dione (AY11) and trans(E)-3,3,3-trifluoro-1-nitroprop-1-ene(FNP10) has been studied, in which the molecular electron density theory using density functional theory methods at the MPWB1K/6-31G(d) computational level was used. Analysis of the global reactivity indices permits us to characterize FNP10 as a strong electrophile and AY11 as a strong nucleophile. Four reactive pathways associated with the ortho/meta regioselective channels and endo/exo stereoselective approaches modes have been explored and characterized in the gas phase and in the benzene solvent. The analysis of the relative energies associated with the different reaction pathways indicates that the 32CA reactions of the azomethine ylide (AY) with the nitroalkene (FNP) is meta regioselective with high endo stereoselectivity. This result is in good agreement with the experimental observations. electron localization function topological analysis of the most favored reactive pathways allows for characterizing the mechanism of this 32CA reactions as a non-concerted two-stage one-step mechanism. Finally, non-covalent interactions and quantum theory of atoms in molecule analyses at the meta/endo transition state structure indicate that the presence of different several weak interactions, namely, CF and NH contributed in favoring the formation of a meta-endo cycloadduct.

We describe a step-by-step protocol and toolkit for the computation of the relative dissociation free energy (RDFE) with the GROMACS molecular dynamics package, based on a novel bidirectional nonequilibrium alchemical approach. The proposed methodology does not require any intervention on the code and allows computing with good accuracy the RDFE between small molecules with arbitrary differences in volume, charge, and chemical topology. The procedure is illustrated for the challenging SAMPL9 batch of host-guest pairs. The article is supplemented by a detailed online tutorial, available at https://procacci.github.io/vdssb_gromacs/NE-RDFE and by a public Zenodo repository available at https://zenodo.org/record/6982932.

The TATA box is a promoter sequence able to interact directly with the components of the basal transcription initiation machinery. We investigate the changes in the electronic and magnetic properties of a TATA-DNA sequence when functionalized with different chemical groups; using the first-principles density functional theory specifically, the TATA-DNA sequences were functionalized with methyl groups (CH3 , methylation), amino groups (NH2 , amination), imine groups (NH, imination), chloroamine groups (NCl2 , chloramination), H-adatom (hydrogenation), and Cl-adatom (chlorination). The functional groups were anchored at nitrogen atoms from adenine and oxygen atoms from thymine at sites pointed as reactive regions. We demonstrated that chemical functionalization induces significant changes in charge transfer, hydrogen bond distance, and hydrogen bond energy. The hydrogenation and imination increased the hydrogen bond energy. Results also revealed that the chemical functionalization of DNA molecules exhibit a ferromagnetic ground state, reaching magnetization up to 4.665 μB and complex magnetic ordering. We further demonstrated that the functionalization could induce tautomerism (proton migration in the base pair systems). The present study provides a theoretical basis for understanding the functionalization further into DNA molecules and visualizing possible future applications.

Easy and effective usage of computational resources is crucial for scientific calculations, both from the perspectives of timeliness and economic efficiency. This work proposes a bi-level optimization framework to optimize the computational sequences. Machine-learning (ML) assisted static load-balancing, and different dynamic load-balancing algorithms can be integrated. Consequently, the computational and scheduling engine of the ParaEngine is developed to invoke optimized quantum chemical (QC) calculations. Illustrated benchmark calculations include high-throughput drug suit, solvent model, P38 protein, and SARS-CoV-2 systems. The results show that the usage rate of given computational resources for high throughput and large-scale fragmentation QC calculations can primarily profit, and faster accomplishing computational tasks can be expected when employing high-performance computing (HPC) clusters.

In electronic structure theory, the charge distribution of a nucleus is usually approximated by point charge, Gaussian function, or homogeneously charged sphere, because they have an analytical nuclear attraction integral (NAI) formula. However, these functions do not always provide good approximations for nuclei with large mass number. The two-parameter Fermi (2pF) distribution and more realistic distributions describe well even nuclei with large mass number but do not have analytical NAI formulas. We propose a new function model called augmented Gaussian 12 (AG12), which has sufficient number of parameters and analytical NAI formulas. With the proposed fitting scheme, the AG12 charge distribution model optimally reproduces 2pF and the more realistic charge distributions. Moreover, AG12 fitted to 2pF model reproduces the energy difference of hydrogen-like ions well between the Gaussian distribution and 2pF models. Calculations using AG12 also suggested necessity to use more realistic nuclear charge distributions than 2pF.

The Quantum Drude Oscillator (QDO) model is a promising candidate for accurately calculating the van der Waals (vdW) interaction. Anisotropic QDO models have recently been used to represent quantum fluctuations of molecular fragments rather than that of single atoms. While this model promises accurate calculation of vdW energy, there is significant room for improvements, such as incorporating a proper fragmentation method, higher-order dispersion corrections, and so forth. The present work attempts to gauge dipole-dipole interactions' ability without fragmentation. A suitable anisotropic damping function is also introduced to work with anisotropic QDO. This revised model accurately predicts the binding energies of vdW complexes for most of the systems considered. This work indicates the limit of dipole approximation for an anisotropic QDO-based model.

In this paper we propose a numerical method to localize many-electron excited states. To characterize the electronic structure of the electronic excited states of a system, quantum chemistry methods typically yield a delocalized description of the excitations. Some a priori localization methods have been developed to provide an intuitive local picture of the excited states. They typically require a good strategy to separate the system of interest from its environment, or a set of a priori localized orbitals, that may reduce their computational accuracy. Here, we introduce an a posteriori method to localize delocalized many-body excited states directly obtained from quantum chemistry calculations. A localization metric for the excited states is defined from their representation as electron-hole pairs, which is encoded in the transition density matrix. This novel a posteriori strategy thus allows to localize excitons within a volume around selected fragments of a complex molecular system without tempering with its quantum chemical treatment. The method is tested on π-stacked oligomers of phenanthrenes and pyrenes. It is found to efficiently localize and separate the excitons according to their character while preserving the information about delocalized many-body states at a low computational cost.

Chemical yield is the percentage of the reactants converted to the desired products. Chemists use predictive algorithms to select high-yielding reactions and score synthesis routes, saving time and reagents. This study suggests a novel graph neural network architecture for chemical yield prediction. The network combines structural information about participants of the transformation as well as molecular and reaction-level descriptors. It works with incomplete chemical reactions and generates reactants-product atom mapping. We show that the network benefits from advanced information by comparing it with several machine learning models and molecular representations. Models included logistic regression, support vector machine, CatBoost, and Bidirectional Encoder Representations from Transformers. Molecular representations included extended-connectivity fingerprints, Morgan fingerprints, SMILESVec embeddings, and textual. Classification and regression objectives were assessed for each model and feature set. The goal of each classification model was to separate zero- and non-zero-yielding reactions. The models were trained and evaluated on a proprietary dataset of 10 reaction types. Also, the models were benchmarked on two public single reaction type datasets. The study was supplemented with analysis of data, results, and errors, as well as the impact of steric factors, side reactions, isolation, and purification efficiency. The supplementary code is available at https://github.com/SoftServeInc/yield-paper.

It is established that the reactive orbital energy theory (ROET) theoretically reproduces the rule-based electronic theory diagrams of organic chemistry by a comparative study on the charge transfer natures of typical organic carbon-carbon and carbon-heteroatom bond formation reactions: aldol, Mannich, α-aminooxylation, and isogyric reactions. The ROET, which is an expansion of the reaction electronic theories (e.g., the frontier orbital theory) in terms of orbital energies, elucidates the reactive orbitals driving reactions and the charge transferability indices of the reactions. Performing the ROET analyses of these reactions shows that the charge transfer directions given in the rule-based diagrams of the electronic theory are reproduced even for the functional groups of charge transfer destinations in all but only two processes for 38 reaction processes. The ROET analyses also make clear the detailed orbital-based pictures of these bond formation reactions: that is, the use of the out-of-plane antibonding π orbitals in acidic conditions (enol-mode) and in-plane antibonding π orbitals in basic conditions (enolate-mode), which explain the experimentally assumed mechanisms such as the π-bond formations in acidic conditions and σ-bond formations at α-carbons in basic conditions. Furthermore, the ROET analyses explicate that the methyl group initially accepts electrons and then donates them to the bond formations in the target reactions. It is, consequently, suggested that the ROET serves a theoretical foundation for the electronic theory of organic chemistry.

The ferromagnetic and antiferromagnetic wave functions of the KMnF3 perovskite have been evaluated quantum-mechanically by using an all electron approach and, for comparison, pseudopotentials on the transition metal and the fluorine ions. It is shown that the different number of α and β electrons in the d shell of Mn perturbs the inner shells, with shifts between the α and β eigenvalues that can be as large as 6 eV for the 3s level, and is far from negligible also for the 2s and 2p states. The valence electrons of F are polarized by the majority spin electrons of Mn, and in turn, spin polarize their 1s electrons. When a pseudopotential is used, such a spin polarization of the core functions of Mn and F can obviously not take place. The importance of such a spin polarization can be appreciated by comparing (i) the spin density at the Mn and F nuclear position, and then the Fermi contact constant, a crucial quantity for the hyperfine coupling, and (ii) the ferromagnetic-antiferromagnetic energy difference, when obtained with an all electron or a pseudopotential scheme, and exploring how the latter varies with pressure. This difference is as large as 50% of the all electron datum, and is mainly due to the rigid treatment of the F ion core. The effect of five different functionals on the core spin polarization is documented.

We present the design and implementation of libkrylov, an open-source library for solving matrix-free eigenvalue, linear, and shifted linear equations using Krylov subspace methods. The primary objectives of libkrylov are flexible API design and modular structure, which enables integration with specialized matrix-vector evaluation "engines." Libkrylov features pluggable preconditioning, orthonormalization, and tunable convergence control. Diagonal (conjugate gradient, CG), Davidson, and Jacobi-Davidson preconditioners are available, along with orthonormal and nonorthonormal (nKs) schemes. All functionality of libkrylov is exposed via Fortran and C application programming interfaces (APIs). We illustrate the performance of libkrylov for eigenvalue calculations arising in time-dependent density functional theory (TDDFT) in the Tamm-Dancoff approximation (TDA) and discuss the convergence behavior as a function of preconditioning and orthonormalization methods.

We present a series of auxiliary basis sets, for the elements Na to Ar, for use in density-fitted Hartree-Fock calculations with the correlation consistent cc-pV(n + d)Z orbital basis sets. Benchmarking on total molecular energies, reaction energies and the spectroscopic constants of the SO molecule demonstrate that the new sets address the deficiencies of using existing auxiliary sets in combination with these orbital basis sets. We also report auxiliary basis sets for Na and Mg matched to cc-pVnZ, along with recommendations for pairing auxiliary basis sets to the cc-pVnZ-F12 basis sets for Hartree-Fock calculations.

Macugen is a therapeutic RNA aptamer against vascular endothelial growth factor (VEGF)-165, the VEGF isoform primarily responsible for angiogenesis. It has been reported that Macugen inhibits angiogenesis by specifically binding to the heparin binding domain (HBD) of VEGF165. The mechanism of the molecular recognition between HBD and Macugen is investigated here using all-atom molecular dynamics simulations. We find that Macugen recognizes HBD by an induced-fit mechanism with major conformational changes in Macugen and almost no changes in the structure of HBD, whereas HBD recognizes Macugen by a conformational selection mechanism.