Natural bond orbital analysis of molecular interactions: Theoretical studies of binary complexes of HF, H2O, NH3, N2, O2, F2, CO, and CO2 with HF, H2O, and NH3

Determining the Factors Accounting for Reaction Selectivity: A Relative Energy Gradient - Interacting Quantum Atoms and Natural Bonding Orbitals Study

Identifying the main physicochemical properties accounting for the course of a reaction is of utmost importance to rationalize chemical syntheses. To this aim, the relative energy gradient (REG) method is an appealing approach because it is an unbiased and automatic process to extract the most relevant pieces of energy information. Initially formulated within the interacting quantum atoms (IQA) framework for a single reaction, here we extend the REG method to natural bond orbitals (NBO) analysis and to the case of two competitive processes. This development enables the determination of the driving forces of any chemical selectivity. We illustrate the extended REG method on the case study of ring opening in cyclobutenes, which is an important instance of the so-called torquoselectivity.

Differing Effects of Nonlinearity around the Proton Acceptor on CH··O and NH··O H-Bond Strength within Proteins

The effects of deviations from nonlinearity around the carbonyl proton acceptor of an amide group are assessed by DFT quantum chemical calculations for both CH··O and NH··O H-bonds. The proton donors are the imidazole functional group of His and the indole of Trp, which are paired respectively with N-methylacetamide and acetamide. The displacement of either CH or NH group toward the carbonyl O sp2 lone pairs stabilizes the system and strengthens the H-bond. But the two donor groups differ in their response to a shift out of the amide plane. While the NH··O H-bond is weakened by this displacement, a substantial strengthening is observed when the CH donor is moved out of this plane, in one direction versus the other. This pattern is explained on the basis of simple Coulombic considerations.

Tetrel Bonding of the Carbenium Ion Forms a Pentacoordinate Carbon Atom

As a flat trigonal species, the CR3 + carbenium ion contains a pair of deep π-holes above and below its molecular plane. In the case of CH3 + a first base will form a covalent bond with the central C, making the combined species tetrahedral. Approach of a second base to the opposite side results in a longer but rather strong noncovalent tetrel bond (TB). While CMe3 + can also form a similar asymmetric complex with a pair of bases, it also has the capacity to form a pair of nearly equivalent TBs, such that the resulting symmetric trigonal bipyramid configuration is only slightly higher in energy. When the three substituents on the central C are phenyl rings, the symmetric configuration with two TBs predominates. These tetrel bonds are quite strong, reaching up to 20 kcal/mol. Adding OPH2 or OCH substituents to the phenyl rings permits the formation of intramolecular C⋅⋅O TBs to the central C, very similar in many respects to the case where these TBs are intermolecular.

Molecular Hydrogen Acts as a Hydrogen Bond Proton Acceptor: From Protonated Betaine Tagging to the Weakest Hydrogen Bond

In an attempt to gain further insights into the intermolecular interactions implied by Rizzo's group's cautionary tale related to molecular tagging in infrared multiple photon dissociation (IRMPD) spectroscopy with molecular messengers [Masson, A. . J. Chem. Phys. 2015, 143, 104313], in the present study, we provide an in-depth analysis of the noncovalent interaction between the molecular hydrogen and protonated betaine molecule in the gas phase. We aim to shed some new light on the fundamental issues concerning the wide diapason of hydrogen-bonding-type intermolecular interactions, with a wide variety of proton acceptors. We demonstrate that in the course of tagging the protonated betaine with molecular hydrogen from the OH group side, it is the σ bond of molecular hydrogen that plays the role of hydrogen-bonding proton acceptor. The tagging thus induces a small yet significant red shift of the protonated betaine O-H stretching mode. We investigate the performance of a wide range of density functional theory (DFT) functionals for the calculation of anharmonic vibrational frequency shifts of the studied system, which are essential for the correct interpretation of the experimental IRMPD data. For an accurate prediction of the OH stretching frequency shifts, specifically designed functionals such as Handy's group HCTH/407 should be applied. The empirical dispersion correction enhances the systematic overestimation of the anharmonic frequency shift, characteristic of the most widely used DFT functionals. Combining the full-wave function approach with the charge field perturbation and natural bond orbital (NBO) deletion analyses, we demonstrate that the frequency shift in the OH-tagged structure is governed by the σHH → σ*OH intermolecular charge transfer. This interaction stabilizes the OH-tagged dimer as well, in contrast to the dipole-quadrupole electrostatic interaction energy term. Topological analysis of the electron density reveals the presence of an intermolecular bond critical point with a positive value of the density Laplacian very close to the lower limit for hydrogen bonds. NCI analyses demonstrate that the OH···H2 interaction is weaker than the intramolecular CH···O one within the protonated betaine molecule, with the through of reduced density gradient appearing at less negative sign(λ2)·ρ values. Analyzing the O-H stretching vibrational potential with the second-generation absolutely localized molecular orbitals energy decomposition analysis (ALMO-EDA 2) revealed that in the case of betaineH(+) tagged from the OH group side, the permanent electrostatics (ΔEelec), polarization (ΔEpol), and charge-transfer (ΔEct) contributions to the total intermolecular interaction energy contribute favorably to the weak hydrogen bond formation and to the red shift of the fundamental O-H stretching frequency, the ΔEct contribution being the most significant in the last context. The Pauli repulsion term, on the other hand, favors an O-H stretching frequency blue shift as a consequence of the vibrational confinement effects.

Lithium ion Speciation in Cyclic Solvents: Impact of Anion Charge Delocalization and Solvent Polarizability

The increasing demand for lithium batteries has triggered the search for safer and more efficient electrolytes. Insights into the atomistic description of electrolytes are critical for relating microscopic and macroscopic (physicochemical) properties. Previous studies have shown that the type of lithium salt and solvent used in the electrolyte influences its performance by dictating the speciation of the ionic components in the system. Here, we investigate the molecular origins of ion association in lithium-based electrolytes as a function of anion charge delocalization and solvent chemical identity. To this end, a family of cyano-based lithium salts in organic solvents, having a cyclic structure and containing carbonyl groups, was investigated using a combination of linear infrared spectroscopy and ab initio computations. Our results show that the formation of contact-ion pairs (CIPs) is more favorable in organic solvents containing either ester or carbonate groups and in lithium salts with an anion having low charge delocalization than in an amide/urea solvent and an anion with large charge delocalization. Ab initio computations attribute the degree of CIP formation to the energetics of the process, which is largely influenced by the chemical nature of the lithium ion solvation shell. At the molecular level, atomic charge analysis reveals that CIP formation is directly related to the ability of the solvent molecule to rearrange its electronic density upon coordination to the lithium ion. Overall, these findings emphasize the importance of local interactions in determining the nature of ion-molecule interactions and provide a molecular framework for explaining lithium ion speciation in the design of new electrolytes.

A density functional theory study on interactions in water-bridged dimeric complexes of lignin

Lignin is the main plant cell wall component responsible for recalcitrance in the process of lignocellulosic biomass conversion into biofuels. The recalcitrance and insolubility of lignin in different reaction media are due in part to the hydrogen bonds and π interactions that hold syringyl (S) and guaiacyl (G) units together and promote the formation of stable water-bridged dimeric complexes (WBDCs): S⋯G and S⋯S, in native lignin. The current understanding of how each type of interaction influences the stability of these complexes within lignin native cell walls is still limited. Here, we found by DFT calculations that hydrogen bonding is more dominant than π-stacking interaction between aromatic rings of WBDCs. Although there is a stronger interaction of hydrogen bonds between subunits and water and higher π-stacking interaction in the S⋯S complex compared to the S⋯G complex, the former complex is less thermodynamically stable than the latter due to the entropic contribution coming from the methoxy substituents in the S-unit. Our results demonstrate that the methoxylation degree of lignin units does not significantly influence the structural geometries of WBDCs; if anything, an enhanced dispersion interaction between ring aromatics results in quasi-sandwich geometries as found in "coiled" lignin structures in the xylem tissue of wood. In the same way as that with ionic liquids, polar solvents can dissolve S-lignin by favorable interactions with the aliphatic hydroxyl group in the α-position as the key site or the aromatic hydroxyl group as the secondary site.

Types of noncovalent bonds within complexes of thiazole with CF4 and SiF4

The five-membered heteroaromatic thiazole molecule contains a number of electron-rich regions that could attract an electrophile, namely the N and S lone pairs that lie in the molecular plane, and π-system areas above the plane. The possibility of each of these sites engaging in a tetrel bond (TB) with CF4 and SiF4, as well as geometries that encompass a CH⋯F H-bond, was explored via DFT calculations. There are a number of minima that occur in the pairing of thiazole with CF4 that are very close in energy, but these complexes are weakly bound by less than 2 kcal mol-1 and the presence of a true TB is questionable. The inclusion of zero-point vibrational energies alters the energetic ordering, which is further modified when entropic effects are added. The preferred geometry would thus be sensitive to the temperature of an experiment. Replacement of CF4 by SiF4 leaves intact most of the configurations, and their tight energetic clustering, the ordering of which is again altered as the temperature rises. But there is one exception in that by far the most tightly bound complex involves a strong Si⋯N TB between SiF4 and the lone pair of the thiazole N, with an interaction energy of 30 kcal mol-1. Even accounting for its high deformation energy and entropic considerations, this structure remains as clearly the most stable at any temperature.

Wolfium bonds in homodimers of MX4Y (M = Mo, W; X = F, Cl, Br; Y = O, S, Se)

The term "wolfium bond" has been recently introduced to describe the noncovalent attraction between an atom of group 6 and a nucleophile via a σ-hole binding site. Crystal structures commonly contain a motif wherein two MX4Y units are arranged in close proximity, where M represents either Mo or W, and X and Y refer to halogen and chalcogen atoms respectively. DFT calculations were thus applied to a wide range of homodimers of these molecules so as to assess their preferred arrangements, and to characterize the types of bonding that are present in each in a systematic manner. The most stable Dual-X configuration is symmetric and contains a pair of equivalent M⋯X bonds. The interaction energies range from -8 to -29 kcal mol-1, and are largest for X = F, Y = O, and M = W. The X electron donor is replaced by Y, and the two wolfium bonds are reduced to one, in the less stable Mono-Y structure, with interaction energies between -2 and -10 kcal mol-1. There is some question as to whether the weaker bonds of this type constitute true wolfium bonds.

Deciphering the Unconventional Reduction of C=N Bonds by Old Yellow Enzymes Using QM/MM

The reduction of C=X (X = N, O) bonds is a cornerstone in both synthetic organic chemistry and biocatalysis. Conventional reduction mechanisms usually involve a hydride ion targeting the less electronegative carbon atom. In a departure from this paradigm, our investigation into Old Yellow Enzymes (OYEs) reveals a mechanism involving transfer of hydride to the formally more electronegative nitrogen atom within a C=N bond. Beyond their known ability to reduce electronically activated C=C double bonds, e.g., in α, β-unsaturated ketones, these enzymes have recently been shown to reduce α-oximo-β-ketoesters to the corresponding amines. It has been proposed that this transformation involves two successive reduction steps and proceeds via imine intermediates formed by the reductive dehydration of the oxime moieties. We employ advanced quantum mechanics/molecular mechanics (QM/MM) simulations, enriched by a two-tiered approach incorporating QM/MM (UB3LYP-6-31G*/OPLS2005) geometry optimization, QM/MM (B3LYP-6-31G*/amberff19sb) steered molecular dynamics simulations, and detailed natural-bond-orbital analyses to decipher the unconventional hydride transfer to nitrogen in both reduction steps and to delineate the role of active site residues as well as of substituents present in the substrates. Our computational results confirm the proposed mechanism and agree well with experimental mutagenesis and enzyme kinetics data. According to our model, the catalysis of OYE involves hydride transfer from the flavin cofactor to the nitrogen atom in oximoketoesters as well as iminoketoesters followed by protonation at the adjacent oxygen or carbon atoms by conserved tyrosine residues and active site water molecules. Two histidine residues play a key role in the polarization and activation of the C=N bond, and conformational changes of the substrate observed along the reaction coordinate underline the crucial importance of dynamic electron delocalization for efficient catalysis.

Influence of Internal Angular Arrangement on Pnicogen Bond Strength

The three Z-X covalent bonds of a ZX3 unit (Z = P, As, Sb, Bi) are normally arranged in a pyramidal structure. Quantum chemical calculations show that pnicogen bonds (ZBs) to the central Z are weakened if ZX3 is flattened, as in the opening of an umbrella. The partial closing of the umbrella has the opposite effect of substantially strengthening these ZBs, even amounting to a 2- or 3-fold magnification in certain cases. The strongest such bonds, wherein Sb and Bi are in a strained configuration within a ZO3CH model system, have interaction energies of 20 kcal/mol with an NH3 base. Most of these systems, whether flattened or more pyramidal, are capable of engaging in three ZBs simultaneously, despite a certain amount of negative cooperativity.

An Exploration of the Hydrogen Bond Donor Ability of Ammonia

Ammonia is an important molecule due to its wide use in the fertiliser industry. It is also used in aminolysis reactions. Theoretical studies of the reaction mechanism predict that in reactive complexes and transition states, ammonia acts as a hydrogen bond donor forming N-H⋅⋅⋅O hydrogen bond. Experimental reports of N-H⋅⋅⋅O hydrogen bond, where ammonia acts as a hydrogen bond donor are scarce. Herein, the hydrogen bond donor ability of ammonia is investigated with three chalcogen atoms i. e. O, S, and Se using matrix isolation infrared spectroscopy and electronic structure calculations. In addition, the chalcogen bond acceptor ability of ammonia has also been investigated. The hydrogen bond acceptor molecules used here are O(CH3 )2 , S(CH3 )2 , and Se(CH3 )2 . The formation of the 1 : 1 complex has been monitored in the N-H symmetric and anti-symmetric stretching modes of ammonia. The nature of the complex has been delineated using Atoms in Molecules analysis, Natural Bond Orbital analysis, and Energy Decomposition Analysis. This work presents the first comparison of the hydrogen bond donor ability of ammonia with O, S, and Se.

Mononuclear half-sandwich nd7 metallo drug complexes based on bidentate N∩N dendritic scaffolds: DFT (B3LYP; BP86 and B3PW91) examination

Through an use of three functionals (B3PW91, B3LYP and BP86) associated to a generic basis set LanL2DZ for transition metals (as well as halogen atoms) and 6-311+G (d,p) for others atoms, an examination of the bonding properties of a series of mononuclear half-sandwich nd⁷ transition metal (anticancer) complexes based on N∩N dendritic scaffolds (L) has been done. Collectively, complexes studied have adopted the piano-stool environment. An examination of the performance of each functional has shown that for the most reliable geometrical analysis of Metal-Nitrogen and Metal-Halogen bonds, the B3LYP and B3PW91 functionalities are suitable respectively. Regardless of the halogen ligand adopted, the B3LYP metal-nitrogen bond lengths are the most widely overestimated. A correlation has been built between the retained charge on each divalent transition metal cation and its metal ion affinity (MIA). Topological examinations reveal the higher instability of metal-N bonds compared to metal-X ones (X = Cl and Br). By the mean of the energy decomposition analysis, a predominant electrostatic character of metal … halogen and [LCP]^- … [MX]⁺ interaction has been demonstrated. The transition metal atom … (hydrophobic) surface (Cp*) interaction is most pronounced for the chloride rhodium complexes of rhodium (combined with (E)-N-(pyridin-2-ylmethylene) Propan-1-amine and 2,2'- dipyridylketone ligands and iridium combined with 2,2'- dipyridylketone ligand. The charge decomposition analysis displays the weakening of the [Formula: see text] bonds in the studied complexes.

Activation of metal-involved halogen bonds and classical halogen bonds in gold(I) catalysis

In gold(I) catalysis, the activation of Au(I) chloride catalysts via chloride abstraction and noncovalent interactions has become a research focus in organometallic catalysis. In this work, taking halogen bond donors (C₄H₂INO₂, C₆F₅I, C₈H₉O₂I) as activators for a Au(I) chloride catalyst (Ph₃PAuCl), the mechanism of the cyclization reaction of propargylic amide was investigated. It was found that there are two activation modes as design principles to obtain the catalytically active species Ph₃PAu⁺: the halogen bond donors activate the Cl atoms of Ph₃PAuCl to form X-I⋯Cl (X = C, N) classical halogen bonds and activate the Au atoms of Ph₃PAuCl to form X-I⋯Au (X = C, N) metal-involved halogen bonds. For the two activation modes, the mechanism of the cyclization reaction of propargylic amide has pathways: the chloride abstraction process of the first step and the 5-exo/6-endo cyclization process of the second step. Both activation modes show good activity for the cyclization reaction with the activation ability of classical halogen bonds being slightly stronger than that of the metal-involved halogen bonds, which is consistent with the strength of the X-I⋯Cl halogen bonds being slightly stronger than that of the X-I⋯Au halogen bonds. Therefore, both metal-involved halogen bonds and classical halogen bonds have important development prospects for the activation of catalysts in gold(I) catalysis.

Factors contributing to halogen bond strength and stretch or contraction of internal covalent bond

The halogen bond formed by a series of Lewis acids TF₃X (T = C, Si, Ge, Sn, Pb; X = Cl, Br, I) with NH₃ is studied by quantum chemical calculations. The interaction energy is closely mimicked by the depth of the σ-hole on the X atom as well as the full electrostatic energy. There is a first trend by which the hole is deepened if the T atom to which X is attached becomes more electron-withdrawing: C > Si > Ge > Sn > Pb. On the other hand, larger more polarizable T atoms are better able to transmit the electron-withdrawing power of the F substituents. The combination of these two opposing factors leaves PbF₃X forming the strongest XBs, followed by CF₃X, with SiF₃X engaging in the weakest bonds. The charge transfer from the NH₃ lone pair into the σ*(TX) antibonding orbital tends to elongate the covalent TX bond, and this force is largest for the heavier X and T atoms. On the other hand, the contraction of this bond deepens the σ-hole at the X atom, which would enhance both the electrostatic component and the full interaction energy. This bond-shortening effect is greatest for the lighter X atoms. The combination of these two opposing forces leaves the T-X bond contracting for X = Cl and Br, but lengthening for I.

Spectroscopic, quantum chemical, molecular docking and molecular dynamics investigations of hydroxylic indole-3-pyruvic acid: a potent candidate for nonlinear optical applications and Alzheimer's drug

In this paper, a complete theoretical investigation of hydroxylic indole-3-pyruvic acid (HIPyA) molecule was performed using the DFT quantum chemical, molecular docking and molecular dynamics calculations. The conformational analysis of HIPyA molecule was carried out using density functional theory quantum chemical calculations. The most stable structure of the studied molecule was predicted by means of DFT/B3LYP method with cc-pVTZ basis set. The simulated vibrational frequencies were assigned and proved to be in agreement with the available experimental FT-IR data. The effects of gas phase and solvents on UV-visible spectra of HIPyA molecule were simulated using TD-DFT/B3LYP method with cc-pVTZ basis set. The analysis of the density of states spectrum validates the frontier molecular orbitals results, which reveals the charge transfer interaction in HIPyA molecule. The molecular electrostatic potential surface confirms the electrophilic and nucleophilic reactive sites of the studied molecule. The natural bond orbital analysis evidences the bioactivity of the studied molecule. The obtained first order hyperpolarizability value is 33.596 times greater than urea, which confirms the nonlinear optical activity of HIPyA molecule. The molecular docking analysis reveals that the studied molecule under interest can act as a potent inhibitor against the amyloid β-protein (Aβ) enzyme, which causes the Alzheimer's disease. The molecular dynamics analysis confirms the reliability of the docking results.Communicated by Ramaswamy H. Sarma.

Adjusting the balance between hydrogen and chalcogen bonds

A complex is assembled which pairs a carboxyl group of X₁COOH with a 1,2,5-chalcogenadiazole ring containing substituents on its C atoms. The OH of the carboxyl group donates a proton to a N atom of the ring to form a OH⋯N H-bond (HB), while its carbonyl O engages in a Y⋯O chalcogen bond (ChB) with the ring in which Y = S, Se, Te. The ChB is strengthened by enlarging the size of the Y atom from S to Se to Te. Placement of an electron-withdrawing group (EWG) X₁ on the acid strengthens the HB while weakening the ChB; the reverse occurs when EWGs are placed on the ring. By selection of the proper substituents on the two units, it is possible to achieve a near perfect balance between the strengths of these two bonds. These bond strengths are also reflected in the NMR spectroscopic properties of the chemical shielding of the various atoms and the coupling between the nuclei directly involved in each bond.

Unexpected Strengthening of the H-Bond Complexes in a Polar Solvent Due to a More Efficient Solvation of the Complex Compared to Isolated Monomers

It is generally assumed that hydrogen-bonded complexes are less stable in solvents than in the gas phase and that their stability decreases with increasing solvent polarity. This assumption is based on the size of the area available to the solvent, which is always smaller in the complex compared to the subsystems, thereby reducing the solvation energy. This reduction prevails over the amplification of the electrostatic hydrogen bond by the polar solvent. In this work, we show, using experimental IR spectroscopy and DFT calculations, that there are hydrogen-bonded complexes whose stability becomes greater with increasing solvent polarity. The explanation for this surprising stabilization is based on the analysis of the charge redistribution in the complex leading to increase of its dipole moment and solvation energy. Constrained DFT calculations have shown a dominant role of charge transfer over polarization effects for dipole moment and solvation energy.

Stability and bonding of carbon(0)-iron-N2 complexes relevant to nitrogenase co-factor: EDA-NOCV analyses

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 C_ring donor, π-C donor) and stronger donor set like CP₃ (σ-C donor) ligands, respectively.

High-Density “Windowpane” Coordination Patterns of Water Clusters and Their NBO/NRT Characterization

Cluster mixture models for liquid water at higher pressures suggest the need for water clusters of higher coordination and density than those commonly based on tetrahedral H-bonding motifs. We show here how proton-ordered water clusters of increased coordination and density can assemble from a starting cyclic tetramer or twisted bicyclic (Möbius-like) heptamer to form extended Aufbau sequences of stable two-, three-, and four-coordinate “windowpane” motifs. Such windowpane clusters exhibit sharply reduced (~90°) bond angles that differ appreciably from the tetrahedral angles of idealized crystalline ice I_h. Computed free energy and natural resonance theory (NRT) bond orders provide quantitative descriptors for the relative stabilities of clusters and strengths of individual coordinative linkages. The unity and consistency of NRT description is demonstrated to extend from familiar supra-integer bonds of the molecular regime to the near-zero bond orders of the weakest linkages in the present H-bond clusters. Our results serve to confirm that H-bonding exemplifies resonance–covalent (fractional) bonding in the sub-integer range and to further discount the dichotomous conceptions of “electrostatics” for intermolecular bonding vs. “covalency” for intramolecular bonding that still pervade much of freshman-level pedagogy and force-field methodology.

Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking

Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.

π-Hole bonding in a new co-crystal hydrate of gallic acid and pyrazine: static and dynamic charge density analysis

A new cocrystal hydrate of gallic acid with pyrazine (4GA, Py, 4H2O; GA4PyW4) was obtained and characterized by single crystal X-ray diffraction. In addition to structure determination, experimental charge density analysis was carried out in terms of Multipole Modelling (MP), X-ray wavefunction refinement (XWR) and maximum entropy method (MEM). As a part of XWR, the structural refinement via Hirshfeld atom refinement was carried out and resulted in O-H bond lengths close to values from neutron diffraction. A systematic comparison of molecular conformations and aromatic interactions in this new cocrystal hydrate was performed with other existing polymorphs of gallic acid. In GA4PyW4, the two symmetry-independent gallic acid molecules have a syn COOH orientation and form the common (COOH)2 dimeric synthon. The carboxyl C atom displays the characteristics of π-holes with electropositive regions above and below the molecular plane and engages in acceptor-donor interactions with oxygen atoms of acidic O-H groups and phenol groups of neighbouring gallic acid molecules. The signature of the π-hole was identified from experimental charge density analysis, both in static density maps in MP and XWR as well as dynamic density in MEM, but it cannot be pinned down to a specific atom-atom interaction. This study presents the first comparison between an XWR and a MEM experimental electron-density determination.

Analysis of Conformational Preferences in Caffeine

High level DLPNO−CCSD(T) electronic structure calculations with extended basis sets over B3LYP−D3 optimized geometries indicate that the three methyl groups in caffeine overcome steric hindrance to adopt uncommon conformations, each one placing a C−H bond on the same plane of the aromatic system, leading to the C−H bonds eclipsing one carbonyl group, one heavily delocalized C−N bond constituent of the fused double ring aromatic system, and one C−H bond from the imidazole ring. Deletion of indiscriminate and selective non-Lewis orbitals unequivocally show that hyperconjugation in the form of a bidirectional −CH3 ⇆ aromatic system charge transfer is responsible for these puzzling conformations. The structural preferences in caffeine are exclusively determined by orbital interactions, ruling out electrostatics, induction, bond critical points, and density redistribution because the steric effect, the allylic effect, the Quantum Theory of Atoms in Molecules (QTAIM), and the non-covalent interactions (NCI), all predict wrong energetic orderings. Tiny rotational barriers, not exceeding 1.3 kcal/mol suggest that at room conditions, each methyl group either acts as a free rotor or adopts fluxional behavior, thus preventing accurate determination of their conformations. In this context, our results supersede current experimental ambiguity in the assignation of methyl conformation in caffeine and, more generally, in methylated xanthines and their derivatives.

On the Ability of Nitrogen to Serve as an Electron Acceptor in a Pnicogen Bond

Whereas pnicogen atoms like P and As have been shown repeatedly to act as electron acceptors in pnicogen bonds, the same is not true of the more electronegative first-row N atom. Quantum calculations assess whether N can serve in this capacity in such bonds and under what conditions. There is a positive π-hole belt that surrounds the central N atom in the linear arrangement of NNNF, NNN-CN, and NNO, which can engage a NH₃ base to form a pnicogen bond with binding energy between 3 and 5 kcal/mol. Within the context of a planar arrangement, the π-hole above the N in NO₂OF, N(CN)₃, and CF₃NO₂ is also capable of forming a pnicogen bond, the strongest of which amounts to 11 kcal/mol with NMe₃ as base. In their pyramidal geometry, NF₃ and N(NO₂)₃ engage with a base through the σ-hole on the central N, with variable binding energies between 2 and 9 kcal/mol. AIM and NBO provide somewhat different interpretations of the secondary interactions that occur in some of these complexes.

σ-Electrons Responsible for Cooperativity and Ring Equalization in Hydrogen-Bonded Supramolecular Polymers

We have quantum chemically analyzed the cooperative effects and structural deformations of hydrogen-bonded urea, deltamide, and squaramide linear chains using dispersion-corrected density functional theory at BLYP-D3(BJ)/TZ2P level of theory. Our purpose is twofold: (i) reveal the bonding mechanism of the studied systems that lead to their self-assembly in linear chains; and (ii) rationalize the C-C bond equalization in the ring moieties of deltamide and squaramide upon polymerization. Our energy decomposition and Kohn-Sham molecular orbital analyses reveal cooperativity in all studied systems, stemming from the charge separation within the σ-electronic system by charge transfer from the carbonyl oxygen lone pair donor orbital of one monomer towards the σ* N-H antibonding acceptor orbital of the neighboring monomer. This key orbital interaction causes the C=O bonds to elongate, which, in turn, results in the contraction of the adjacent C-C single bonds that, ultimately, makes the ring moieties of deltamide and squaramide to become more regular. Notably, the π-electron delocalization plays a much smaller role in the total interaction between the monomers in the chain.

A full-dimensional ab initio intermolecular potential energy surface and rovibrational spectra for OC-HF and OC-DF

We present a full-dimensional ab initio intermolecular potential energy surface (IPES) for the OC-HF van der Waals complex. 3167 ab initio points were computed at the frozen-core (FC) explicitly correlated coupled cluster [FC-CCSD(T)-F12b] level, with the augmented correlation-consistent polarized valence quadruple-zeta basis set plus bond functions. Basis set superposition error correction was also considered by the full counterpoise procedure. Gaussian process regression (GPR) was used to map out the potential energy surface, while a multipole expansion method was employed to smooth the ab initio noise of intermolecular potential in the long range. The global minimum of -1248.364 cm^-1 was located at the linear configuration with the C atom pointing toward the H atom of the HF molecule. In addition, a local minimum of -602.026 cm^-1 was found at another linear configuration with the O atom pointing toward the H atom of the HF molecule. The eigenstates were calculated on the vibrational averaged four-dimensional IPESs with the mixed radial discrete variable representation/angular finite basis representation method and Lanczos propagation algorithm. The dissociation energy D₀ was calculated to be 701.827 cm^-1, well reproducing the experimental value of 732 ± 2 cm^-1. The dipole moment surfaces were also fitted by GPR from 3132 ab initio points calculated using the coupled cluster method [CCSD(T)] with AVTZ basis set plus bond functions. The frequencies and relative line intensities of rovibrational transitions in the HF (DF) and CO stretching bands were further calculated and compared well with the experimental results. These results indicate the high fidelity of the new IPES.

Lewis Structures from Open Quantum Systems Natural Orbitals: Real Space Adaptive Natural Density Partitioning

Building chemical models from state-of-the-art electronic structure calculations is not an easy task, since the high-dimensional information contained in the wave function needs to be compressed and read in terms of the accepted chemical language. We have already shown ( Phys. Chem. Chem. Phys. 2018, 20, 21368) how to access Lewis structures from general wave functions in real space by reformulating the adaptive natural density partitioning (AdNDP) method proposed by Zubarev and Boldyrev ( Phys. Chem. Chem. Phys. 2008, 10, 5207). This provides intuitive Lewis descriptions from fully orbital invariant position space descriptors but depends on not immediately accessible higher order cumulant density matrices. By using an open quantum systems (OQS) perspective, we here show that the rigorously defined OQS fragment natural orbitals can be used to build a consistent real space adaptive natural density partitioning based only on spatial information and the system's one-particle density matrix. We show that this rs-AdNDP approach is a cheap, efficient, and robust technique that immerses electron counting arguments fully in the real space realm.

Theoretical investigation on hydrogen bond interaction between adrenaline and hydrogen sulfide

In this study, we elucidated the formation of hydrogen bond between adrenaline (AD) and hydrogen sulfide utilizing computational studies. Six potential complexes were studied including geometrical parameters, energy, vibrational frequency, topological analysis, natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM), and NMR analysis. Moreover, these calculations were examined through DFT/ωB97XD/6-311G++(d,p) level. It was found that there are no indication on formation on hydrogen bonding between the two catecholic OHs where the one formed between the amino group and the hydroxyl oxygen atom of adrenaline monomer was broken in AS₁ to form two new interactions namely SH^...N and O₁H₁^...S, while it retained in other complexes. Furthermore, the bond became stronger due to cooperativity in AS₃ and AS₆, for the presence of withdrawing effect of the phenyl ring, the H-bonds formed with the side chain oxygen atom. The adrenaline and H₂S interaction was experimentally examined via FT-IR spectrometry and thin layer chromatography for confirmation of our theoretical study. Graphical abstract.

Anatomy of Base Pairing in DNA by Interacting Quantum Atoms

The formation of purine and pyrimidine base pairs (BPs), which contributes to shaping of the canonical and noncanonical 3D structures of nucleic acids, is one the most investigated phenomena in chemistry and life sciences. In this contribution, the anatomy of the bond energy (BDE) of the base-pairing interaction in 39 different arrangements found experimentally or predicted for DNA structures containing the four common nucleobases (A, C, G, T) in their neutral or protonated forms is described in light of the theory of interacting quantum atoms within the context of the quantum theory of atoms in molecules. The interplay of individual energy components involved in the three stages of the bond formation process (structural deformation, electron-density promotion, and intermolecular interaction) is studied. We recognized that for the neutral BPs, variations in the kinetic and electrostatic contributions to the BDE are rather negligible, leaving the exchange-correlation energy as the main stabilizing component. It is shown that the contribution of the exchange-correlation term can be recovered by including atoms that are formally assumed to be hydrogen bonded (primary interaction). In contrast, to recover the electrostatic component of interaction, one must consider both the primary and secondary (formally nonbonded atoms) interatomic interactions. The results of our study were employed to design new types of BPs with altered bonding anatomy. We demonstrate that improving the electrostatic characteristics of the BPs does not necessarily result in greater interaction energies if weak secondary hydrogen bonding is destroyed. However, the main tuning factor for systems with conserved interacting faces (primary interactions) is the electrostatic component of the interaction energy resulting from the secondary atom-atom electrostatics.

Understanding noncovalent bonds and their controlling forces

The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.

Exploring the Origin of the Axial-Conformation Preferences in the 3-Halopiperidinium Cations: the Importance of the Coulombic Potential Energies

Although there are some published conclusions in the literature concerning the origin of the axial-conformation preference in 3-fluoropiperidinium cations (charge-dipole orientation effect), the origin of the axial-conformation preferences in the 3-halopiperidinium cations [halogen = F (1), Cl (2), Br (3)] has remained an open question. To explore the origin of the axial-conformation preferences in compounds 1-3, we assessed the roles and contributions of the hyperconjugative interactions, the Coulombic electrostatic interactions, the electrostatic model associated with dipole-dipole interactions, and the steric effects associated with the Pauli exchange-type repulsions on the conformational properties of compounds 1-3 utilizing the G3MP2, LC-ωPBE, and B3LYP methods and natural bond orbital (NBO) interpretations. Natural Coulombic potential energies are in favor of the axial conformations of compounds 1-3, and justify their corresponding total energy differences. The through-space hyperconjugative interactions between the donor lone pairs of halogen atoms (LP3X) and the acceptor antibonding orbitals of H-N bonds [σ*(H-N) ⊕], LP3X → σ*(H-N) ⊕, increase from compound 1 to compound 3. The inspection of the dipole moments of the parallel C-X and H-N bonds in the axial conformations of compounds 1-3 revealed that the variations of their corresponding four-center dipole-dipole interactions correlate well with their corresponding conformational behaviors. The steric effects associated with the Pauli exchange-type repulsions are strongly in favor of the equatorial conformations of compounds 1-3. Accordingly, the charge-dipole orienting effect associated with the four-center dipole-dipole interactions is a dominant factor in the conformational behaviors of compounds 1-3.

Unusually strong hydrogen bond cooperativity in particular (H2O)20 clusters

Drawing upon an intuitive charge-transfer-based picture of hydrogen bonding, we demonstrate that cooperativity effects acting in concert can lead to unusually strong hydrogen bonds in neutral water clusters. The structure, vibrational, and NMR properties of a (H2O)20 pentagonal dodecahedron cluster containing such a strong hydrogen bond were studied using second-order perturbation theory and density functional theory. The hydrogen bond length was found to be shorter than 2.50 Å. A large redshift of over 2000 cm-1 with respect to the isolated water molecule was predicted for the OH stretching frequency of the donor water molecule. A large downfield shift to 13.5 ppm of the isotropic part of the 1H magnetic shielding tensor together with an unusually large shielding anisotropy of 49.9 ppm was obtained. The hydrogen bond energy was calculated using symmetry-adapted perturbation theory and was found to be more than three times stronger than a typical hydrogen bond in liquid water.

Bond Order Densities in Real Space

In this contribution we introduce the concept of bond order density (BOD) on the basis of a previous work on natural adaptive orbitals. We show that BODs may be used to visualize both the global spatial distribution of the covalent bond order and its eigencomponents, which we call bond(ing) channels. BODs can be equally computed at correlated and noncorrelated levels of theory and in ground or excited states, thus offering an appealing description of bond-forming, bond-breaking, and bond-evolution processes. We show the power of the approach by examining a number of homo- and heterodiatomics, including the controversial existence of a fourth bonding component in dicarbon, by analyzing a few interesting bonding situations in polyatomics and chemical transformations, and by exemplifying exotic bonding behaviors in simple excited electronic states.

Non-covalent interactions with inverted carbon: a carbo-hydrogen bond or a new type of hydrogen bond?

Crystal structure analysis and quantum chemical calculations enabled us to discover a new non-covalent interaction, coined as carbo-hydrogen bond (C_H-bond).