Deformation Electron Density Research Articles

Supramolecular assembly governed by tetrel, CN⋅⋅⋅π and other weak noncovalent interactions in two acrylonitrile derivatives with D-π-A topology: Crystallography, optical properties and theoretical studies

Two D-π-A acrylonitriles, (Z)-3-(4-methoxyphenyl)-2-(pyridin-4-yl)acrylonitrile (1) and (Z)-3-(4-piperidin-1-yl)-2-(pyridin-4-yl)acrylonitrile (2), were synthesized to investigate how the varying donor moieties affect their structural and optical properties. Compound 1 crystallized with two crystallographically independent molecules, each showing different orientations of the methoxy group, and exhibited herringbone molecular arrangement in the solid-state. This structure is stabilized by CH···N/π interactions, π-stacking, cyano···π stacking (CN···π) and a σ-hole tetrel bond involving the C and O atoms of the methoxy group. Compound 2 crystallized with a single molecule in the asymmetric unit and displayed columnar packing mode. This structure is stabilized intermolecular CH···N interactions, where all nitrogen atoms serve as acceptors, as well as by intermolecular CH···π interactions and π-stacking between adjacent pyridyl rings. Hirshfeld surfaces and 2D-fingerprint plots revealed the effect of donor moieties on the intermolecular interactions. The energetics of the molecular dimers observed in these structures were characterized by both CLP-PIXEL energy and DFT calculations. The nature of the tetrel bond was characterized using molecular electrostatic surface potential and deformation electron density maps. Theoretical charge density analysis was performed to characterize the noncovalent interactions in various molecular dimers of 1 and 2. The absorption spectra of compounds 1 and 2 exhibit a 40 nm red-shift in solution, attributed to the presence of the piperidyl moiety in compound 2.

Transferability of Buckingham Parameters for Short-Range Repulsion between Topological Atoms.

The repulsive part of the Buckingham potential, with parameters A and B, can be used to model deformation energies and steric energies. Both are calculated using the interacting quantum atom energy decomposition scheme where the latter is obtained from the former by a charge-transfer-based energy correction. These energies relate to short-range interactions, specifically the deformation of electron density and steric hindrance, respectively, when topological atoms approach each other. In this work, we calculate and fit the energies of carbonyl carbon, carbonyl oxygen, and, where possible, amine nitrogen atoms to the repulsive part of the Buckingham potential for 26 molecules. We find that while the steric energies of all atom pairs studied display exponential behavior with respect to distance, some deformation energy data do not. The obtained parameters are shown to be transferable by calculating root-mean-square errors of fitted potentials with respect to energy data of the same atom in, as far as possible, all other molecules from our data set. We observed that 36% and 10% of these errors were smaller than 4 kJ mol-1 for steric and deformation energy, respectively. Thus, we find that steric energy parameters are more transferable than deformation energy parameters. Finally, we speculate about the physical meaning of the A and B parameters and the implications of the strong exponential and exponential-linear piecewise relationships that we observe between them.

Intramolecular steric and relaxation analysis of nitrogen clusters

Electron deformation density analysis were performed for ten nitrogen clusters NX (X = 4–12,14), where multiple types of fragmentations were considered for each cluster as interaction between a single isolated nitrogen molecule and the rest of cluster. Two components of electronic deformation density including steric or kinetic energy pressure and orbital relaxation were analyzed to reveal deformation density distributions and the corresponding displaced charges as quantitative description. Results show dominance of relaxation over steric interaction from both qualitative and quantitative displaced charges standpoints. Topological analysis of deformation density is also accomplished and critical points and steric paths were identified.

Ru-Doped MoS2 Monolayer for Exhaled Breath Detection on Early Lung Cancer Diagnosis: A First-Principles Investigation.

Nanosensor-based patient exhaled breath detection is a practical and effective way to detect lung cancer early. In this paper, a Ru-doped MoS2 monolayer (Ru-MoS2) is proposed as a promising novel biosensor based on first-principles theory for the detection of three typical early stage lung cancer exhaled volatile organic compounds, namely, C3H4O, C3H6O, and C5H8. Replacement of a S atom in the MoS2 monolayer with a Ru dopant atom to form a stable Ru-MoS2 monolayer with a binding energy of -4.78 eV is further demonstrated by the thermostability and chemical stability analysis as well as improving the adsorption performance of the system for three VOCs. The adsorption configuration structures, adsorption properties, and electronic behavior of the Ru-MoS2 monolayer are investigated by electron deformation density and density of states analysis to gain a comprehensive understanding of the physicochemical properties as sensing material. The results show that the adsorption energies of the Ru-MoS2 monolayer for C3H4O, C3H6O, and C5H8 are 3.42, -1.53, and -2.80 eV, respectively, all of which are chemisorption with excellent adsorption performance. The sensitivities for the three VOCs could be up to 1.09, 140.50, and 5.90, respectively, and the band structure and work function further elucidate the sensing mechanism of the Ru-MoS2 monolayer as a resistive gas sensor. The type and concentration of these exhaled breaths may reflect changes in the patient's physiological and biochemical status and may serve as a probe for the diagnosis of lung cancer. The results in this work could provide a guidance for researchers to explore the practical applications in the early diagnosis of lung cancer by gas sensors.

Exploring the effect of substituents on the supramolecular assemblies built by non-covalent interactions in three closely related 1,3,4-oxadiazole-2(3H)-thione derivatives: An evaluation of antimicrobial and anti-proliferative activities

Three closely related 1,3,4-oxadiazole-2(3H)-thione N-Mannich bases were synthesized and characterized by spectroscopic and single crystal X-ray diffraction methods. X-ray analysis reveals that the title molecules adopt l-shaped conformation, and a slight structural deviation around substituent groups is noted. The Hirshfeld surface and 2D fingerprint plots demonstrate the effect of substituents (piperidine, morpholine, and thiomorpholine) on the intermolecular interactions. The CLP-PIXEL energy analysis identified the most significant interactions in the molecular dimers (that characterize the crystal packing) with respect to the total intermolecular interaction energies. These dimers are held together by various non-covalent interactions including C–H⋅⋅⋅S/N/O/Cl/π interactions in addition to unconventional lone pair⋅⋅⋅π interactions. A molecule with thiomorpholine substituent is favoured by two σ-hole interactions (Cl⋅⋅⋅Cl halogen bond and S⋅⋅⋅N chalcogen bond) in the solid state. Furthermore, the molecular electrostatic potential (MEP) surfaces and deformation electron density help to describe the existence of σ-hole on the Cl and thione S atoms. Noncovalent interaction index (NCI) and quantum theory of atoms in molecules (QTAIM) methods are used to delineate the nature of observed noncovalent interactions in the molecular dimers. In vitro data of antibacterial and anti-proliferative activities indicate that compound with morpholine substituent showed a moderate antibacterial activity against all tested Gram-positive bacterial strains. However, molecules with piperidine and thiomorpholine showed notable effectiveness against the HepG-2 cell line. Molecular docking analysis was performed with two liver cancer targets, VEGFR2 and RET, in order to understand the interactions between the ligand and the active site residues of these targets.

Atomic bonding states of metal and semiconductor elements

In this paper, we use density functional theory (DFT) to calculate the deformation electron density of 46 metal and semiconductor elements. The binding-energy and bond-charge model (BBC) model is combined with the tight-binding and density-functional–tight-binding approaches to obtain quantitative information about atomic bonding at the atomic scale and to understand the contributions and effects of deformation energy density, energy shifts, and atomic bonding on the Hamiltonian. The bonding state is obtained through energy shift and deformation charge density. The BBC model involving no assumptions or freely adjustable parameters, has led to consistency between predictions and experimental observations of the cohesive energy and energy density of nanosolids.

Fluorine versus Hydroxyl in Supramolecular Space: Effect of Organic Fluorine in Molecular Conformation, Lattice Cohesive Energies, and Receptor Binding in a Series of α-Fluoroketones

We examine the effect of organic fluorine in the molecular conformation and supramolecular packing in a series of α-fluoroketones in comparison to the analogous α-hydroxyketones. Crystal structures of a series of seven α-fluoroketone analogues have been analyzed using single-crystal XRD, and their crystal-packing features have been investigated using a variety of computational tools. Analysis of molecular conformations in this series of α-fluoroketone structures, along with conformational energy scans, revealed a preference for a near-antiperiplanar conformation for α-fluoroketones as opposed to a syn conformation in their α-hydroxy analogues. A quantitative analysis of intermolecular interaction motifs such as C–H···F, C–H···O, C–H···π, C–F···π, etc. in terms of interaction energies and electron density topological parameters from a QTAIM (quantum theory of atoms in molecules) approach reveal their relative strengths and distance dependence. Electron localization function (ELF) and deformation density maps bring out the electrostatic nature of weak interactions involving organic fluorine. Lattice energy values estimated using the CE-B3LYP method show dominant contributions from dispersion in all these structures, which are around 3–4-fold higher than the electrostatic contribution. While the lattice energy values of the α-fluoroketones are found to be lower than those of their hydroxy analogues, a molecular docking study with a common protein receptor site reveals comparable docking scores for α-fluoroketones with respect to the analogous α-hydroxyketones.

Metal-Involving Halogen Bonding Confirmed Using DFT Calculations with Periodic Boundary Conditions

The cocrystallization of trans-[PtI2(NCN(CH2)5)2] and iodoform (CHI3) yields crystalline adduct trans-[PtI2(NCN(CH2)5)2]∙2CHI3, the structure of which was studied via single-crystal X-ray diffractometry (XRD). In the XRD structure of trans-[PtI2(NCN(CH2)5)2]∙2CHI3, apart from rather predictable C–H∙∙∙I hydrogen bonds (HBs) and C−I∙∙∙I halogen bonds (XBs) with the iodide ligands, we identified C–I∙∙∙Pt metal-involving XBs, where the platinum center functions as an XB acceptor (that includes a metal dz2-orbital) toward the σ-holes of I atoms of CHI3. DFT calculations (PBE-D3/jorge-TZP-DKH with plane waves in the GAPW method) were carried out in the CP2K program for isolated molecules, complex–iodoform clusters, and crystal models with periodic boundary conditions, where the noncovalent nature and the existence of the interactions were confirmed using charge analysis, Wiberg bond indexes, and QTAIM topology analysis of electron density, whereas the philicities of the noncovalent partners were proved using charge analysis, electron localization function, electron density deformation, and one-electron potential projections, as well as electron density/electrostatic potential profiles for cluster models and electrostatic potential surfaces (ρ = 0.001 a.u.) for isolated molecules.

Enhanced oxygen reduction reaction activity by utilizing carbon nanotube intramolecular junctions

DFT calculations are performed to study the enhanced oxygen reduction reaction (ORR) activity by utilizing carbon nanotube intramolecular junctions (IMJs). The obtained results suggest that the adsorption of ORR species on the basal carbon of the pristine nanotubes (armchair and zigzag structures) is too weak, but significant enhancement of adsorption energy could be found on the same position of two types of typical IMJ structures (straight and bent junctions), with the values closer to Pt(111). Furthermore, ORR curves catalyzed by two IMJs all become downhill in the relative energy diagram, suggesting the spontaneous nature of the catalytic process. These obtained results indicate that IMJs possess higher catalytic activity towards ORR. Total electron density and deformation electron density analysis reveal that the improved adsorption of ORR species could be caused the electrostatic interaction between the adsorbed ORR species and IMJs, where the electrons transfer from the latter to the former.

Adsorption and Sensing Performances of Pristine and Au-Decorated Gallium Nitride Monolayer to Noxious Gas Molecules: A DFT Investigation.

In this study, the adsorption of noxious gas molecules (NO, Cl2, and O3) on GaN and Au-decorated GaN was systematically scrutinized, and the adsorption energy, bond length, charge, density of state (DOS), partial density of state (PDOS), electron deformation density (EDD), and orbitals were analyzed by the density functional theory (DFT) method. It is found that the interaction between NO and pristine GaN is physical adsorption, while GaN chemically reacts with Cl2 and O3. These observations suggest that pristine GaN may be a candidate for the detection of Cl2 and O3. The highly activated Au-decorated GaN can enhance the adsorption performance toward NO and convert the physical adsorption for NO into chemical adsorption, explaining the fact that precious metal doping is essential for regulating the electronic properties of the substrate material. This further confirms the well-established role of Au-decorated GaN in NO gas-sensing applications. In addition, the adsorption performance of Au-decorated GaN for Cl2 and O3 molecules is highly improved, which provides guidance to scavenge toxic gases such as Cl2 and O3 by the Au-decorated GaN material.

Relativistic Spin-Orbit Electronegativity and the Chemical Bond Between a Heavy Atom and a Light Atom.

Relativistic effects are known to alter the chemical bonds and spectroscopic properties of heavy-element compounds. In this work, we introduce the concept of spin-orbit (SO) electronegativity of a heavy atom, as reflected by an SO-induced change in the interatomic distance between the heavy atom (HA) and a neighboring light atom (LA). We provide a transparent interpretation of these SO effects by using the concept of spin-orbit electron deformation density (SO-EDD). Spin-orbit coupling at the HA induces rearrangement of the electron density for the scalar-relativistically optimized geometry that, in turn, exerts a new force on the LA. The resulting expansion or contraction of the HA-LA bond depends on the nature and electron configuration of the HA. In addition, we quantify the change in atomic electronegativity induced by SO coupling for a series of hydrides, thereby complementing the SO-EDD picture. The trends in the SO-induced electronegativity and the HA-LA bond length across the periodic table of elements are demonstrated and interpreted, and also linked, intuitively, with the SO-induced NMR shielding at the LA.

Inclusion of More Physics Leads to Less Data: Learning the Interaction Energy as a Function of Electron Deformation Density with Limited Training Data.

Machine learning (ML) approaches to predicting quantum mechanical (QM) properties have made great strides toward achieving the computational chemist's holy grail of structure-based property prediction. In contrast to direct ML methods, which encode a molecule with only structural information, in this work, we show that QM descriptors improve ML predictions of dimer interaction energy, both in terms of accuracy and data efficiency, by incorporating electronic information into the descriptor. We present the electron deformation density interaction energy machine learning (EDDIE-ML) model, which predicts the interaction energy as a function of Hartree-Fock electron deformation density. We compare its performance with leading direct ML schemes and modern DFT methods for the prediction of interaction energies for dimers of varying charge type, size, and intermolecular separation. Under a low-data regime, EDDIE-ML outperforms other direct ML schemes and is the only model readily transferrable to larger, more complex systems including base pair trimers and porous cages. The underlying physical connection between the density and interaction energy enables EDDIE-ML to reach an accuracy comparable to modern DFT functionals in fewer training data points compared to other ML methods.

Molecular dynamics simulation of the interface interaction and mechanical properties of PYX and polymer binder

The interaction between four polymer binder molecules and 2,6-dipicrylamino-3,5-dinitropyridine (PYX) molecules was determined through the analysis of surface electrostatic potential and deformation electron density. The binding energy, mechanical properties, and cohesive energy density (CED) of Polymer Bonded Explosives (PBXs) based on PYX at different temperatures were studied. By comparing the binding energies of four polymer binders and three PYX crystal surfaces at five temperatures, it was found that the surface of PYX (011) was the most suitable surface, and the binding energy of EPDM (Ethylene Propylene Diene Monomer) and PYX (011) was the strongest by comparing the four polymer-binding molecules with the surface of PYX (011) at the same temperature. The CED values and distribution of CED for four PYX-based PBXs were analyzed with the change in temperature, and the conclusion was drawn that temperature had little influence on CED values. The descending order of CED values of four PYX-based PBXs at the same temperature was as follows: PYX/F2641 > PYX/F246G > PYX/F2311 > PYX/EPDM. At 298 K, the addition of polymer binders significantly changed the mechanical properties of PYX and reduced the stiffness and deformation resistance of the system. In addition, the C12–C44 value of the four systems was positive, which meant that the system was ductile. The order of toughness and ductility is as follows: PYX/F246G > PYX/F2311 > PYX/F2641 > PYX/EPDM. The addition of the polymer binder was helpful for the stability of the explosive. The theoretical detonation velocity and detonation pressure of the PBX systems were calculated.

Dinitrogen Binding Relevant to FeMoco of Nitrogenase: Clear Visualization of σ‐Donation and π‐Backdonation from Deformation Electron Densities around Carbon/Silicon‐Iron Site

AbstractDinitrogen (N2) binding and electron transfer reduction of N2 to ammonia (NH3) by the FeMoco cofactor of the nitrogenase enzyme are captivating. They are a part of the textbook for general chemistry. The nature of N2 bonding by reduced FeMoco is speculated based on the experimental evidence. The inorganic core MoFe7S9C1− possesses a Fe6(μ6‐C4−) unit. The mode of N2‐binding at one of the Fe‐centers of the elusive Fe6(μ6‐C4−) unit and the role of light element C4− is intriguing. In the past, the mode of N2‐binding and the kinetics of N2 reduction have been studied by spectroscopic and other tools. Herein, we report on the energy decomposition analysis coupled with natural orbital for chemical valence (EDA‐NOCV) calculations/analyses to shed light on the deeper insight of the N2 binding and especially on the influence of the C‐atom of previously reported Fe‐complexes with an EP3 donor set (E=C, Si). The role of the C‐atom in the iron‐carbon site has been studied by elaboration with deformation electron densities. The intrinsic interaction energy of the bond between Fe and N2 and pairwise orbital interactions between them have been quantitatively estimated. The influence of σ‐donation of three phosphine ligands and their effects on the Fe−N2 bond have been thoroughly studied.

5-Fluoro-1,2,3-triazole motif in peptides and its electronic properties.

The 5-fluoro triazole amino acid scaffold prepared by halogen exchange has been incorporated into peptides. From the X-ray diffraction of the 5-fluoro triazole motif, the main observation was an important localization on one side of the negative potential surface. The fluorine atom reveals a cylindrical shape in its deformation electron density.

On the transfer of theoretical multipole parameters for restoring static electron density and revealing and treating atomic anharmonic motion. Features of chemical bonding in crystals of an isocyanuric acid derivative

The crystal and electronic structure of an isocyanuric acid derivative was studied by high-resolution single-crystal X-ray diffraction within the Hansen–Coppens multipole formalism. The observed deformation electron density shows signs of thermal smearing. The experimental picture meaningfully assigned to the consequences of unmodelled anharmonic atomic motion. Straightforward simultaneous refinement of all parameters, including Gram–Charlier coefficients, resulted in more significant distortion of apparent static electron density, even though the residual density became significantly flatter and more featureless. Further, the method of transferring multipole parameters from the model refined against theoretical structure factors as an initial guess was employed, followed by the subsequent block refinement of Gram–Charlier coefficients and the other parameters. This procedure allowed us to appropriately distinguish static electron density from the contaminant smearing effects of insufficiently accounted atomic motion. In particular, some covalent bonds and the weak π...π interaction between isocyanurate moieties were studied via the mutual penetration of atomic-like kinetic and electrostatic potential φ-basins with complementary atomic ρ-basins. Further, local electronic temperature was applied as an advanced descriptor for both covalent bonds and noncovalent interactions. Total probability density function (PDF) of nuclear displacement showed virtually no negative regions close to and around the atomic nuclei. The distribution of anharmonic PDF to a certain extent matched the residual electron density from the multipole model before anharmonic refinement. No signs of disordering of the sulfonyl group hidden in the modelled anharmonic motion were found in the PDF.

Size-Dependent πg + πu Combination Band Intensities of Polyynes C2nH2 (n = 1-9) Analyzed by the Local CCH Bending and the Linear Response Functions.

Polyynes (C2nH2) show the unusually strong πg + πu combination bands in the infrared absorption spectra. We calculated them as the first overtone of the local CCH bending; the strong intensities are interpreted as a consequence of the large-amplitude bending vibration of the acidic acetylenic hydrogen combined with the size-dependent π electron conjugation. Our theoretical calculations show that the absorption intensity increases steadily and their increase rate is gradually slowed down by increasing the number of acetylene units up to n = 9. However, the calculated vibrational wavenumber converges quickly in agreement with the experimental observation. The second-order electron density deformation caused by the local CCH bending was analyzed using the linear response functions, including the linear and nonlinear contributions, to explain the n dependence. The easily polarizable π electron density caused two kinds of deformation-dominant but dark δxx-yy type and minor but bright σ type. Both of them exhibit interesting zigzag sign alternations, consistent with the law of alternating polarity of Coulson and Longuet-Higgins. The electron density polarization in these intra- and interacetylene units induces a large axial component molecular dipole moment, contributing to the intensity that increases with n. The difference between the curvilinear and rectilinear bending coordinates is interpreted within the present theoretical scheme.

Orbital-Free Quantum Crystallographic View on Noncovalent Bonding: Insights into Hydrogen Bonds, π⋅⋅⋅π and Reverse Electron Lone Pair⋅⋅⋅π Interactions.

A detailed analysis of a complete set of the local potentials that appear in the Euler equation for electron density is carried out for noncovalent interactions in the crystal of a uracil derivative using experimental X-ray charge density. The interplay between the quantum theory of atoms in molecules and crystals and the local potentials and corresponding inner-crystal electronic forces of electrostatic and kinetic origin is explored. Partitioning of crystal space into atomic basins and atomic-like potential basins led us to the definite description of interatomic interaction and charge transfer. Novel physically grounded bonding descriptors derived within the orbital-free quantum crystallography provided the detailed examination of π-stacking and intricate C=O⋅⋅⋅π interactions and nonclassical hydrogen bonds present in the crystal. The donor-acceptor character of these interactions is revealed by analysis of Pauli and von Weizsäcker potentials together with well-known functions, e. g., deformation electron density and electron localization function. In this way, our analysis throws light on aspects of these closed-shell interactions hitherto hidden from the description.

Application of the Molecular Invariom Model for the Study of Interactions Involving Fluorine Atoms in the {{text{Yb}}_{{text{2}}}^{{{text{II}}}}(\u03bc2-OCH(CF3)2)3(\u03bc3-OCH(CF3)2)2YbIII(OCH(CF3)2)2(THF)(Et2O)} Complex

The electron density distributions obtained by the quantum-chemical (density functional theory) calculations and molecular invariom model in the trimeric ytterbium complex with the hexafluoroisopropoxide ligands {{text{Yb}}_{{text{2}}}^{{{text{II}}}}(μ2-OR)3(μ3-OR)2YbIII(OR)2(THF)(Et2O)} (I) (where R is CH(CF3)2, and THF is tetrahydrofuran) are compared. The main topological characteristics of the electron density at the critical points (3, –1) corresponding to the interactions of the ytterbium atoms in the coordination sphere obtained using two studied approaches demonstrate excellent agreement. The maximum divergence between the density functional calculations and molecular invariom model is observed for the intramolecular interactions involving the fluorine atoms (F···F, F···H, and F···O) in the structure of complex I. Geometry optimization leads to a higher number of these interactions in the complex. The energy corresponding to these interactions also increases. However, the main topological characteristics for the F···X interactions (X = F, H, O), which can be localized in the framework of both methods, remain within the transferability index range. An analysis of the deformation electron density shows that the Fδ–···Fδ– interactions are determined by the correspondence of the region of electron density concentration on one of the fluorine atoms to the region of electron density depletion on the second fluorine atom regardless of the method of measuring the electron density distribution.

Superatomic Signature and Reactivity of Silver Clusters with Oxygen: Double Magic Ag 17 – with Geometric and Electronic Shell Closure

Understanding the stability and reactivity of silver clusters toward oxygen provides insights to design new materials of coinage metals with atomic precision. Herein, we report a systematic study o...