Potential Energy Surfaces of HN(CH)SX:CO2 for X = F, Cl, NC, CN, CCH, and H: N···C Tetrel Bonds and O···S Chalcogen Bonds

(Pyridin-2-ylmethyl)triel Derivatives as Masked Frustrated Lewis Pairs. Interactions and CO2 -Sequestration

The isolated (pyridin-2-ylmethyl)triel derivatives (triel=B, Al and Ga) show an intramolecular N⋅⋅⋅Tr triel bond as shown by compounds found in the Cambridge Structural Database and DFT calculations. The possibility to use them as masked frustrated Lewis pairs (mFLP) has been explored theoretically concerning their reaction with CO2 . The adduct formation proceeds in two steps. In the first one, the (pyridin-2-ylmethyl)triel derivatives break the intramolecular N⋅⋅⋅Tr bond assisted by CO2 and in the second step the adduct is formed with Tr-O and N-C covalent bonds. The corresponding energy minima and transition states (TS) of the reaction have been characterized and analyzed. The distortion/interaction model analysis of the stationary points indicates that the whole process can be divided in two parts: reorganization of the mFLP in the first steps of the reaction while the reaction with CO2 (associated to the distortion of this molecule) is more important in the formation of the final adduct. In all cases studied, the final products are more stable than the starting molecules that combine with reasonable TS energies indicating that these reactions can occur.

Maximal occupation by bases of π-hole bands surrounding linear molecules

Linear molecules such as CO₂ contain a positive π-hole ring that surrounds C on the molecule's equator. Quantum calculations examine the question as to how many bases can simultaneously bind to this ring. Linear molecules examined are TO₂ , where T = C, Si, Ge, Sn; bases are NCH and NH₃ . CO₂ engages in the weakest of the tetrel bonds, and can bind up to three NCH and two NH₃ . Unlike σ-hole tetrel bonds, Si forms the strongest tetrel bonds, with interaction energies as high as 43 kcal/mol with NH₃ . But like GeO₂ , SiO₂ can sustain only two bases in its equatorial ring. The π-hole ring of SnO₂ can engage in up to four tetrel bonds with either NCH or NH₃ , even though these bonds are weaker than those with GeO₂ or SiO₂ . As all of these complexes cast TO₂ in the role of multiple electron acceptor, the resulting negative cooperativity makes each successive bond weaker than its predecessor as bases are added, as well as reducing the magnitude of the central molecule's π-hole.

Anatomy of π-hole bonds: Linear systems

The list of σ-hole bonds is long and growing, encompassing both H-bonds and its closely related halogen, chalcogen, etc., sisters. These bonds rely on the asymmetric distribution of electron density, whose depletion along the extension of a covalent bond leaves a positive region of electrostatic potential from which these bonds derive their name. However, the density distributions of other molecules contain analogous positive regions that lie out of the molecular plane known as π-holes, which are likewise capable of engaging in noncovalent bonds. Quantum calculations are applied to study such π-hole bonds that involve linear molecules, whose positive region is a circular belt surrounding the molecule, rather than the more restricted area of a σ-hole. These bonds are examined in terms of their most fundamental elements arising from the spatial dispositions of their relevant molecular orbitals and the π-holes in both the total electron density and the electrostatic potential to which they lead. Systems examined comprise tetrel, chalcogen, aerogen, and triel bonds, as well as those involving group II elements, with atoms drawn from various rows of the Periodic Table. The π-hole bonds established by linear molecules tend to be weaker than those of comparable planar systems.

Versatility of the Cyano Group in Intermolecular Interactions

Several cyano groups are added to an alkane, alkene, and alkyne group so as to construct a Lewis acid molecule with a positive region of electrostatic potential in the area adjoining these substituents. Although each individual cyano group produces only a weak π-hole, when two or more such groups are properly situated, they can pool their π-holes into one much more intense positive region that is located midway between them. A NH3 base is attracted to this site, where it forms a strong noncovalent bond to the Lewis acid, amounting to as much as 13.6 kcal/mol. The precise nature of the bonding varies a bit from one complex to the next but typically contains a tetrel bond to the C atoms of the cyano groups or the C atoms of the linkage connecting the C≡N substituents. The placement of the cyano groups on a cyclic system like cyclopropane or cyclobutane has a mild weakening effect upon the binding. Although F is comparable to C≡N in terms of electron-withdrawing power, the replacement of cyano by F substituents substantially weakens the binding with NH3.

Calculated coupling constants 1 J(X-Y) and 1 K(X-Y), and fundamental relationships among the reduced coupling constants for molecules Hm X-YHn , with X, Y ═ 1 H, 7 Li, 9 Be, 11 B, 13 C, 15 N, 17 O, 19 F, 31 P, 33 S, and 35 Cl

Equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) calculations have been performed to determine coupling constants ¹ J(X-Y) for 65 molecules H_m X-YH_n , with X,Y ═ ¹ H, ⁷ Li, ⁹ Be, ¹¹ B, ¹³ C, ¹⁵ N, ¹⁷ O, ¹⁹ F, ³¹ P, ³³ S, and ³⁵ Cl. The computed ¹ J(X-Y) values are in good agreement with available experimental data. The reduced coupling constants ¹ K(X-Y) have been derived from ¹ J(X-Y) by removing the dependence on the magnetogyric ratios of X and Y. Patterns are found for the reduced coupling constants on a ¹ K(X-Y) surface that are related to the positions of X and Y in the periodic table.

Growth Pattern, Stability, and Properties of Complexes of C2H5OH and nCO2 (n = 1-5) Molecules: A Theoretical Study

This work is dedicated to theoretically investigate the formation process of C2H5OH···nCO2 (n = 1-5) complexes and to shed light on the nature of interactions formed under the variation of CO2 concentration. It is found that CO2 molecules tend to locate around the polarized -OH group to interact with the lone pairs of the O atom. The interaction of ethanol with three CO2 molecules (C2H5OH···3CO2) induces the most stable structure in the sequence considered. The atoms in molecules (AIM), NCIplot, and natural bond orbital (NBO) analyses point out that the Oethanol···CCO2 tetrel bond overcomes hydrogen, chalcogen, and CO2···CO2 tetrel-bonded interactions and mainly contributes to the strength of C2H5OH···nCO2 (n = 1-5) complexes. All intermolecular interactions in the examined complexes are weakly noncovalent, and their positive cooperativity is evaluated to be slightly weaker than that of CO2 pure systems. SAPT2+ and molecular electrostatic potential (MEP) calculations indicate that the electrostatic force is the main factor underlying the attractive interplay in the complexes of C2H5OH and CO2.

Complexes H2 CO:PXH2 and HCO2 H : PXH2 for X=NC, F, Cl, CN, OH, CCH, CH3 , and H: Pnicogen Bonds and Hydrogen Bonds

Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate H₂ CO : PXH₂ pnicogen-bonded complexes and HCO₂ H : PXH₂ complexes that are stabilized by pnicogen bonds and hydrogen bonds, with X=NC, F, Cl, CN, OH, CCH, CH₃ , and H. The binding energies of these complexes exhibit a second-order dependence on the O-P distance. DFT-SAPT binding energies correlate linearly with MP2 binding energies. The HCO₂ H : PXH₂ complexes are stabilized by both a pnicogen bond and a hydrogen bond, resulting in greater binding energies for the HCO₂ H : PXH₂ complexes compared to H₂ CO : PXH₂ . Neither the O-P distance across the pnicogen bond nor the O-P distance across the hydrogen bond correlates with the binding energies of these complexes. The nonlinearity of the hydrogen bonds suggests that they are relatively weak bonds, except for complexes in which the substituent X is either CH₃ or H. The pnicogen bond is the more important stabilizing interaction in the HCO₂ H : PXH₂ complexes except when the substituent X is a more electropositive group. EOM-CCSD spin-spin coupling constants ^1p J(O-P) across pnicogen bonds in H₂ CO:PXH₂ and HCO₂ H : PXH₂ complexes increase as the O-P distance decreases, and exhibit a second order dependence on that distance. There is no correlation between ^2h J(O-P) and the O-P distance across the hydrogen bond in the HCO₂ H : PXH₂ complexes. ^2h J(O-P) coupling constants for complexes with X=CH₃ and H have much greater absolute values than anticipated from their O-P distances.

Not Only Hydrogen Bonds: Other Noncovalent Interactions

In this review, we provide a consistent description of noncovalent interactions, covering most groups of the Periodic Table. Different types of bonds are discussed using their trivial names. Moreover, the new name “Spodium bonds” is proposed for group 12 since noncovalent interactions involving this group of elements as electron acceptors have not yet been named. Excluding hydrogen bonds, the following noncovalent interactions will be discussed: alkali, alkaline earth, regium, spodium, triel, tetrel, pnictogen, chalcogen, halogen, and aerogen, which almost covers the Periodic Table entirely. Other interactions, such as orthogonal interactions and π-π stacking, will also be considered. Research and applications of σ-hole and π-hole interactions involving the p-block element is growing exponentially. The important applications include supramolecular chemistry, crystal engineering, catalysis, enzymatic chemistry molecular machines, membrane ion transport, etc. Despite the fact that this review is not intended to be comprehensive, a number of representative works for each type of interaction is provided. The possibility of modeling the dissociation energies of the complexes using different models (HSAB, ECW, Alkorta-Legon) was analyzed. Finally, the extension of Cahn-Ingold-Prelog priority rules to noncovalent is proposed.

Nature of the Interaction of Pyridines with OCS. A Theoretical Investigation

Ab initio calculations were carried out to investigate the interaction between para-substituted pyridines (X-C₅H₄N, X=NH₂, CH₃, H, CN, NO₂) and OCS. Three stable structures of pyridine.OCS complexes were detected at the MP2=full/aug-cc-pVDZ level. The A structure is characterized by N…S chalcogen bonds and has binding energies between −9.58 and −12.24 kJ/mol. The B structure is bonded by N…C tetrel bond and has binding energies between −10.78 and −11.81 kJ/mol. The C structure is characterized by π-interaction and has binding energies between −10.76 and −13.33 kJ/mol. The properties of the systems were analyzed by AIM, NBO, and SAPT calculations. The role of the electrostatic potential of the pyridines on the properties of the systems is outlined. The frequency shift of relevant vibrational modes is analyzed.

Lead(ii) coordination polymers driven by pyridine-hydrazine donors: from anion-guided self-assembly to structural features

This work unveils an indispensable role of London dispersion forces and relativistic effects in tetrel and covalent bonds of the type Pb–X (X = O, N, S, I), which drives formation of extended architectures of lead(ii) coordination polymers.

Theoretical Studies of IR and NMR Spectral Changes Induced by Sigma-Hole Hydrogen, Halogen, Chalcogen, Pnicogen, and Tetrel Bonds in a Model Protein Environment

Various types of σ-hole bond complexes were formed with FX, HFY, H2FZ, and H3FT (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) as Lewis acid. In order to examine their interactions with a protein, N-methylacetamide (NMA), a model of the peptide linkage was used as the base. These noncovalent bonds were compared by computational means with H-bonds formed by NMA with XH molecules (X = F, Cl, Br, I). In all cases, the A-F bond, which lies opposite the base and is responsible for the σ-hole on the A atom (A refers to the bridging atom), elongates and its stretching frequency undergoes a shift to the red with a band intensification, much as what occurs for the X-H bond in a H-bond (HB). Unlike the NMR shielding decrease seen in the bridging proton of a H-bond, the shielding of the bridging A atom is increased. The spectroscopic changes within NMA are similar for H-bonds and the other noncovalent bonds. The C=O bond of the amide is lengthened and its stretching frequency red-shifted and intensified. The amide II band shifts to higher frequency and undergoes a small band weakening. The NMR shielding of the O atom directly involved in the bond rises, whereas the C and N atoms both undergo a shielding decrease. The frequency shifts of the amide I and II bands of the base as well as the shielding changes of the three pertinent NMA atoms correlate well with the strength of the noncovalent bond.

N…C and S…S Interactions in Complexes, Molecules, and Transition Structures HN(CH)SX:SCO, for X = F, Cl, NC, CCH, H, and CN

Ab initio Møller-Plesset perturbation theory (MP2)/aug'-cc-pVTZ calculations have been carried out in search of complexes, molecules, and transition structures on HN(CH)SX:SCO potential energy surfaces for X = F, Cl, NC, CCH, H, and CN. Equilibrium complexes on these surfaces have C1 symmetry, but these have binding energies that are no more than 0.5 kJ·mol-1 greater than the corresponding Cs complexes which are vibrationally averaged equilibrium complexes. The binding energies of these span a narrow range and are independent of the N-C distance across the tetrel bond, but they exhibit a second-order dependence on the S-S distance across the chalcogen bond. Charge-transfer interactions stabilize all of these complexes. Only the potential energy surfaces HN(CH)SF:SCO and HN(CH)SCl:SCO have bound molecules that have short covalent N-C bonds and significantly shorter S…S chalcogen bonds compared to the complexes. Equation-of-motion coupled cluster singles and doubles (EOM-CCSD) spin-spin coupling constants 1tJ(N-C) for the HN(CH)SX:SCO complexes are small and exhibit no dependence on the N-C distance, while 1cJ(S-S) exhibit a second-order dependence on the S-S distance, increasing as the S-S distance decreases. Coupling constants 1tJ(N-C) and 1cJ(S-S) as a function of the N-C and S-S distances, respectively, in HN(CH)SF:SCO and HN(CH)SCl:SCO increase in the transition structures and then decrease in the molecules. These changes reflect the changing nature of the N…C and S…S bonds in these two systems.

Effects of Halogen, Chalcogen, Pnicogen, and Tetrel Bonds on IR and NMR Spectra

Complexes were formed pairing FX, FHY, FH2Z, and FH3T (X = Cl, Br, I; Y = S, Se, Te; Z = P, As, Sb; T = Si, Ge, Sn) with NH3 in order to form an A⋯N noncovalent bond, where A refers to the central atom. Geometries, energetics, atomic charges, and spectroscopic characteristics of these complexes were evaluated via DFT calculations. In all cases, the A-F bond, which is located opposite the base and is responsible for the σ-hole on the A atom, elongates and its stretching frequency undergoes a shift to the red. This shift varies from 42 to 175 cm-1 and is largest for the halogen bonds, followed by chalcogen, tetrel, and then pnicogen. The shift also decreases as the central A atom is enlarged. The NMR chemical shielding of the A atom is increased while that of the F and electron donor N atom are lowered. Unlike the IR frequency shifts, it is the third-row A atoms that undergo the largest change in NMR shielding. The change in shielding of A is highly variable, ranging from negligible for FSnH3 all the way up to 1675 ppm for FBr, while those of the F atom lie in the 55-422 ppm range. Although smaller in magnitude, the changes in the N shielding are still easily detectable, between 7 and 27 ppm.