A structural and theoretical study of the intermolecular interactions in 8‐hydroxyquinolinium‐7‐carboxylate monohydrate

In the title compound, C₁₀H₇NO₃·H₂O, the zwitterionic organic molecules and the water molecules are connected by N—H...O and O—H...O hydrogen bonds to form ribbons, and π–π stacking interactions expand these ribbons into a three‐dimensional net. The energies of these hydrogen bonds adopt values typical for mildly weak interactions (3.33–7.75 kcal mol⁻¹; 1 kcal mol⁻¹ = 4.184 kJ mol⁻¹). The total π–π stacking interactions between aromatic molecules can be classified as mildly strong (energies of 15.3 and 33.9 kcal mol⁻¹), and they are made up of multiple constituent π–π interactions between six‐membered rings. The short intermolecular C—H...O contact between two zwitterionic molecules is nonbonding in character.     

The HOX⋯SO2 (X=F,Cl, Br,I) Binary Complexes: Implications for Atmospheric Chemistry

Sulfur dioxide and hypohalous acids (HOX, X=F, Cl, Br, I) are ubiquitous molecules in the atmosphere that are central to important processes like seasonal ozone depletion, acid rain, and cloud nucleation. We present the first theoretical examination of the HOX⋯SO₂ binary complexes and the associated trends due to halogen substitution. Reliable geometries were optimized at the CCSD(T)/aug-cc-pV(T+d)Z level of theory for HOF and HOCl complexes. The HOBr and HOI complexes were optimized at the CCSD(T)/aug-cc-pV(D+d)Z level of theory with the exception of the Br and I atoms which were modeled with an aug-cc-pwCVDZ-PP pseudopotential. 27 HOX⋯SO₂ complexes were characterized and the focal point method was employed to produce CCSDT(Q)/CBS interaction energies. Natural Bond Orbital analysis and Symmetry Adapted Perturbation Theory were used to classify the nature of each principle interaction. The interaction energies of all HOX⋯SO₂ complexes in this study ranged from 1.35 to 3.81 kcal mol⁻¹. The single-interaction hydrogen bonded complexes spanned a range of 2.62 to 3.07 kcal mol⁻¹, while the single-interaction halogen bonded complexes were far more sensitive to halogen substitution ranging from 1.35 to 3.06 kcal mol⁻¹, indicating that the two types of interactions are extremely competitive for heavier halogens. Our results provide insight into the interactions between HOX and SO₂ which may guide further research of related systems.     

Hydrogen bonding in the mixed HF/HCl dimer: Is it better to give or receive?

The ClH⋯FH and FH⋯ClH configurations of the mixed HF/HCl dimer (where the donor⋯acceptor notation indicates the directionality of the hydrogen bond) as well as the transition state connecting the two configurations have been optimized using MP2 and CCSD(T) with correlation consistent basis sets as large as aug‐cc‐pV(5 + d)Z. Harmonic vibrational frequencies confirmed that both configurations correspond to minima and that the transition state has exactly one imaginary frequency. In addition, anharmonic vibrational frequencies computed with second‐order vibrational perturbation theory (VPT2) are within 6 cm⁻¹ of the available experimental values and deviate by no more than 4 cm⁻¹ for the complexation induced HF frequency shifts. The CCSD(T) electronic energies obtained with the largest basis set indicate that the barrier height is 0.40 kcal mol⁻¹ and the FH⋯ClH configuration lies 0.19 kcal mol⁻¹ below the ClH⋯FH configuration. While only modestly attenuating the barrier height, the inclusion of either the harmonic or anharmonic zero‐point vibrational energy effectively makes both minima isoenergetic, with the ClH⋯FH configuration being lower by only 0.03 kcal mol⁻¹. © 2018 Wiley Periodicals, Inc.     

Proton shuttle efficiency of bicarbonate: A theoretical study on tautomerization and CO2 hydration

The efficiency of bicarbonate molecule (HCO₃⁻) as a proton shuttle in the tautomerization and (non)enzymatic CO₂ hydration reactions has been investigated with the aid of computational chemistry methods (DFT and ab initio). The results revealed that bicarbonate can decrease the barrier height of tautomerization (keto-enol, azo-hydrazo and imine-amine) more than 70%. This value is around 45% for water molecules. Also, HCO₃⁻ can catalyze the CO₂ hydration both inside (enzymatic) and outside (nonenzymatic) the active site of human carbonic anhydrases II (HCA II). In the absence of enzyme, bicarbonate molecule can lower the CO₂ hydration from ∼50 kcal mol⁻¹ in the gas phase to ∼14 kcal mol⁻¹ in the aqueous media. This reaction maintains its barrier (∼15 kcal mol⁻¹) for bicarbonate-Zn complex in the active site of enzyme; it has been observed that amino acid residues, mainly Thr199 and Glu106, are actively involved in the proton transfer network and facilitate CO₂ hydration ability of bicarbonate.     

Energetic Ordering of Hydrogen Bond Strengths in Methanol-Water Clusters: Insights via Molecular Tailoring Approach

In this work, we examine the strength of various types of individual hydrogen bond (HB) in mixed methanol-water M_nW_m, (n+m=2 to 7) clusters, with an aim to understand the relative order of their strength, using our recently proposed molecular tailoring-based approach (MTA). Among all the types of HB, it is observed that the O_M−H…O_W HBs are the strongest (6.9 to 12.4 kcal mol⁻¹). The next ones are O_M−H…O_M HBs (6.5 to 11.6 kcal mol⁻¹). The O_W−H…O_W (0.2 to 10.9 kcal mol⁻¹) and O_W−H…O_M HBs (0.3 to 10.3 kcal mol⁻¹) are the weakest ones. This energetic ordering of HBs is seen to be different from the respective HB energies in the dimer i. e., O_M−H…O_M (5.0 to 6.0 kcal mol⁻¹)>O_W−H…O_M (1.5 to 6.0 kcal mol⁻¹)>O_M−H…O_W (3.8 to 5.6 kcal mol⁻¹)>O_W−H…O_W (1.2 to 5.0 kcal mol⁻¹). The plausible reason for the difference in the HB energy ordering may be attributed to the increase or decrease in HB strengths due to the formation of cooperative or anti-cooperative HB networks. For instance, the cooperativity contribution towards the different types of HB follows: O_M−H…O_W (2.4 to 8.6 kcal mol⁻¹)>O_M−H…O_M (1.3 to 6.3 kcal mol⁻¹)>O_W−H…O_W (−1.0 to 6.5 kcal mol⁻¹)>O_W−H…O_M (−1.2 to 5.3 kcal mol⁻¹). This ordering of cooperativity contribution is similar to the HB energy ordering obtained by the MTA-based method. It is emphasized here that, the interplay between the cooperative and anti-cooperative contributions are indispensable for the correct energetic ordering of these HBs.     

Predicting Dinitrogen Activation via Transition-Metal-Involved [4+2] Cycloaddition Reaction

As the strongest triple bond in nature, the N≡N triple bond activation has always been a challenging project in chemistry. On the other hand, since the award of the Nobel Prize in Chemistry in 1950, the Diels-Alder reaction has served as a powerful and widely applied tool in the synthesis of natural products and new materials. However, the application of the Diels-Alder reaction to dinitrogen activation remains less developed. Here we first demonstrate that a transition-metal-involved [4+2] Diels-Alder cycloaddition reaction could be used to activate dinitrogen without an additional reductant by density functional theory calculations. Further study reveals that such a dinitrogen activation by 1-metalla-1,3-dienes screened out from a series of transition metal complexes (38 species) according to the effects of metal center, ligand, and substituents can become favorable both thermodynamically (with an exergonicity of 28.2 kcal mol⁻¹) and kinetically (with an activation energy as low as 13.8 kcal mol⁻¹). Our findings highlight an important application of the Diels-Alder reaction in dinitrogen activation, inviting experimental chemists’ verification.     

Theoretical Investigations on the Agostic Interactions of the Molybdenum and Manganese Complexes

The essential participation of agostic interactions in C−H bond activation, cyclometallation and other catalytic processes has been widely observed. To quantitatively evaluate the Mo−H−C agostic interaction in the Mo β/γ- agostomers [CpMo(CO)₂(PiPr₃)]⁺ ( Mo , 1 and Mo , 2 ) and the Mn−H−C agostic interaction in the Mn α/ϵ-agostomers [(C₆H₉]Mo(CO)₃] ( Mn , 1 and Mn , 2 ), the comprehensive density functional theory (DFT) theoretical investigations were performed. Results indicated that the Mo β-agostomer 1 is only favorable by 0.5 kcal mol⁻¹ than Mo γ-agostomer 2 , and the Gibbs barrier for their interconversion was 9.1 kcal mol⁻¹. A slightly higher Gibbs barrier of 12.7 kcal mol⁻¹ for the isomerization between the Mn α/ϵ-agostomers was also obtained. The relatively strong agostic interactions in Mo β-agostomer 1 and Mn α-agostomer 1 were further verified by the AIM (Atoms-In-Molecules) analyses and the NAdOs (natural adaptive orbitals) analyses. The findings on the agostic interaction presented in this study are believed to benefit the understandings of the agostic interaction involved catalytic processes and to promote the development of new organometallic complexes.     

Computational and dynamic NMR investigation of 2,2-dimesityl-1,1,1,3,3,3-hexamethyltrisilane

The structure and rotational barrier for the mesityl-silicon bond of 2,2-dimesityl-1,1,1,3,3,3-hexamethyltrisilane have been investigated by ¹H- and ¹³C-variable temperature nuclear magnetic resonance (NMR) as well as by density functional theory structural calculations. The calculations show that the lowest energy structure has C₂ symmetry with nonequivalent ortho methyl groups, consistent with the crystal structure and solution NMR. The nonequivalent ortho methyl groups exchange through a C_s transition state with a calculated relative free energy of 11.0 kcal mol⁻¹. The barrier for this rotation found by dynamic NMR is 13.4 ± 0.2 kcal mol⁻¹ at 298 K.     

Group 15 and 16 Nitrene-Like Pnictinidenes

Pnictinidenes are an increasingly relevant species in main group chemistry and generally exhibit proclivity for the triplet electronic ground state. However, the elusive singlet electronic states are often desired for chemical applications. We predict the singlet-triplet energy differences (ΔE_ST=E_Singlet−E_Triplet) of simple group 15 and 16 substituted pnictinidenes (Pn−R; Pn=P, As, Sb, or Bi) with highly reliable focal-point analyses targeting the CCSDTQ/CBS level of theory. The only cases we predict to have favorable singlet states are P−PH₂ (−3.2 kcal mol⁻¹) and P−NH₂ (−0.2 kcal mol⁻¹). ΔE_ST trends are discussed in light of the geometric predictions as well as qualitative natural bond order analysis to elucidate some of the important electronic structure features. Our work provides a rigorous benchmark for the ΔE_ST of fundamental Pn−R moieties and provides a firm foundation for the continued study of heavier pnictinidenes.     

Preparing Gold(I) for Interactions with Proton Donors: The Elusive [Au]⋅⋅⋅HO Hydrogen Bond

MP2 and DFT calculations with correlation consistent basis sets indicate that isolated linear anionic dialkylgold(I) complexes form moderately strong (ca. 10 kcal mol^?1) Au???H hydrogen bonds with single H₂O molecules as donors in the absence of sterically demanding substituents. Relativistic effects are critically important in the attraction. Such bonds are significantly weaker in neutral, strong σ‐donor N‐heterocyclic carbene (NHC) complexes (ca. 5 kcal mol^?1). The overall association (>11 kcal mol^?1), however, is strengthened by co‐operative, synergistic classical hydrogen bonding when the NHC ligands bear NH units. Further manipulation of the interaction by ligands positioned trans to the carbene, is possible.     

A structural and theoretical study of intermolecular interactions in nicotinohydrazide dihydrochloride

In the title compound [systematic name: 3‐(azaniumylcarbamoyl)pyridinium dichloride], C₆H₉N₃O²⁺·2Cl⁻, the ions are connected by N—H...Cl hydrogen bonds to form layers and C—H...Cl interactions expand the layers into a three‐dimensional net. The energies of the N—H...Cl interactions range from typical for very weak interactions (0.17 kcal mol⁻¹) to those observed for relatively strong interactions (29.1 kcal mol⁻¹). C—H...Cl interactions can be classified as weak and mildly strong (energies ranging from 2.2 to 8.2 kcal mol⁻¹). Despite the short contacts existing between the parallel aromatic rings of the cations, π–π interactions do not occur.     

Photochemical Generation of Strained Cycloalkynes from Methylenecyclopropanes

The hydrocarbons 1‐cyclopentylidene‐1a,9b‐dihydro‐1H ‐cyclopropa[l ]phenanthrene and 1‐cyclobutylidene‐1a,9b‐dihydro‐1H ‐cyclopropa[l ]phenanthrene undergo photolysis in solution at ambient temperature to produce cyclohexyne and cyclopentyne, respectively. These strained cycloalkynes, formed via the putative cycloalkylidenecarbenes, were intercepted as Diels–Alder adducts. Calculations at the CCSD(T)/cc‐pVTZ//B3LYP/6‐31+G* level of theory show that singlet cyclopentylidenecarbene has to overcome a barrier of 9.1 kcal mol⁻¹ to rearrange into cyclohexyne (with ΔE for ring expansion=−15.1 kcal mol⁻¹). By contrast, cyclobutylidenecarbene only needs to surmount a barrier of 1.6 kcal mol⁻¹ to rearrange into cyclopentyne (with ΔE for ring expansion=−6.2 kcal mol⁻¹).     

Theoretical and experimental studies of the diketene system: Product branching decomposition rate constants and energetics of isomers

The kinetics and mechanism for the thermal decomposition of diketene have been studied in the temperature range 510–603 K using highly diluted mixtures with Ar as a diluent. The concentrations of diketene, ketene, and CO₂ were measured by FTIR spectrometry using calibrated standard mixtures. Two reaction channels were identified. The rate constants for the formation of ketene (k₁) and CO₂ (k₂) have been determined and compared with the values predicted by the Rice–Ramsperger–Kassel–Marcus (RRKM) theory for the branching reaction. The first-order rate constants, k₁ (s⁻¹) = 10^{15.74 ± 0.72} exp(−49.29 (kcal mol⁻¹) (±1.84)/RT) and k₂ (s⁻¹) = 10^{14.65 ± 0.87} exp(−49.01 (kcal mol⁻¹) (±2.22)/RT); the bulk of experimental data agree well with predicted results. The heats of formation of ketene, diketene, cyclobuta-1,3-dione, and cyclobuta-1,2-dione at 298 K computed from the G2M scheme are −11.1, −45.3, −43.6, and −40.3 kcal mol⁻¹, respectively. © 2007 Wiley Periodicals, Inc. Int J Chem Kinet 39: 580–590, 2007     

Predicting Small Molecule Activation including Catalytic Hydrogenation of Dinitrogen Promoted by a Dual Lewis Acid

For decades, N₂ activation and functionalization have required the use of transition metal complexes. Thus, it is one of the most challenging projects to activate the abundant dinitrogen through metal-free systems under mild conditions. Here, we demonstrate a proof-of-concept study on the catalytic hydrogenation of dinitrogen (with activation energy as low as 15.3 kcal mol⁻¹) initiated by a dual Lewis acid (DLA) via density functional theory (DFT) calculations. In addition, such a DLA could be also used to activate a series of small molecules including carbon dioxide, formaldehyde, N-ethylenemethylamine, and acetonitrile. It is found that aromaticity plays an important role in stabilizing intermediates and products. Our findings provide an alternative approach to N₂ activation and functionalization, highlighting a great potential of DLA for small molecule activation.     

Understanding Regium Bonds and their Competition with Hydrogen Bonds in Au2:HX Complexes

A theoretical study of the regium and hydrogen bonds (RB and HB, respectively) in Au₂:HX complexes has been carried out by means of CCSD(T) calculations. The theoretical study shows as overall outcome that in all cases the complexes exhibiting RB are more stable that those with HB. The binding energies for RB complexes range between −24 and −180 kJ ⋅ mol^−1, whereas those of the HB complexes are between −6 and −19 kJ ⋅ mol⁻¹. DFT-SAPT also indicated that HB complexes are governed by electrostatics, but RB complexes present larger contribution of the induction term to the total attractive forces. ¹⁹⁷Au chemical shifts have been calculated using the relativistic ZORA Hamiltonian.     

Two Three‐Dimensional Metal‐Organic Frameworks Constructed from Alkaline Earth Metal Cations (Sr and Ba) and 5‐Nitroisophthalicacid – Synthesis,Charaterization, and Thermochemistry

Two MOFs of [Sr^II(5‐NO₂‐BDC)(H₂O)₆] ( 1 ) and [Ba^II(5‐NO₂‐BDC)(H₂O)₆] ( 2 ) have been synthesized in water using alkaline earth metal salts and the rigid organic ligand 5‐NO₂‐H₂BDC. The compounds were characterized by elemental analysis, infrared spectrum, thermal analysis, and X‐ray crystallography. Crystal structure analyses have shown that the two complexes are isostructural as evidenced by IR spectra and TG‐DTA. Both compounds present three‐dimensional frameworks built up from infinite chains of edge‐sharing twelve‐membered rings through O–H···O hydrogen bonds. The specific heat capacities of the title complexes have been determined by an improved RD496‐III microcalorimeter with the values of (109.29 ± 0.693) J mol⁻¹ K⁻¹ and (81.162 ± 0.858) J mol⁻¹ K⁻¹ at 298.15 K, and the molar enthalpy changes of the formation reactions of complexes at 298.15 K were calculated as (4.897 ± 0.008) kJ mol⁻¹ and (2.617 ± 0.009) kJ mol⁻¹, respectively.     

Towards the Accurate Thermodynamic Characterization of Enzyme Reaction Mechanisms

We employed QM/MM molecular dynamics (MD) simulations to characterize the rate-limiting step of the glycosylation reaction of pancreatic α-amylase with combined DFT/molecular dynamics methods (PBE/def2-SVP : AMBER). Upon careful choice of four starting active site conformations based on thorough reactivity criteria, Gibbs energy profiles were calculated with umbrella sampling simulations within a statistical convergence of 1–2 kcal ⋅ mol⁻¹. Nevertheless, Gibbs activation barriers and reaction energies still varied from 11.0 to 16.8 kcal ⋅ mol⁻¹ and −6.3 to +3.8 kcal ⋅ mol⁻¹ depending on the starting conformations, showing that despite significant state-of-the-art QM/MM MD sampling (0.5 ns/profile) the result still depends on the starting structure. The results supported the one step dissociative mechanism of Asp197 glycosylation preceded by an acid-base reaction by the Glu233, which are qualitatively similar to those from multi-PES QM/MM studies, and thus support the use of the latter to determine enzyme reaction mechanisms.     

Quantitative decomposition of resonance-assisted hydrogen bond energy in β-diketones into resonance and hydrogen bonding (π- and σ-) components using molecular tailoring and function-based approaches

Using the molecular tailoring and function-based approaches allows one to divide the energy of the O─H⋯O═C resonance-assisted hydrogen bond in a series of the β-diketones into resonance and hydrogen bonding components. The magnitude of the resonance component is assessed as about 6 kcal mol⁻¹. This value increases by ca. 1 kcal mol⁻¹ on going from the weak to strong resonance-assisted hydrogen bonding. The magnitude of the hydrogen bonding component varies in the wide range from 2 to 20 kcal mol⁻¹ depending on the structure of the β-diketone in question.     

Generating and Trapping Metalla‐N‐Heterocyclic Carbenes

By means of a combined experimental and theoretical approach, the electronic features and chemical behavior of metalla‐N‐heterocyclic carbenes (MNHCs, N‐heterocyclic carbenes containing a metal atom within the heterocyclic skeleton) have been established and compared with those of classical NHCs. MNHCs are strongly basic (proton affinity and pK_a values around 290 kcal mol^?1 and 36, respectively) with a narrow singlet–triplet gap (around 23 kcal mol^?1). MNHCs can be generated from the corresponding metalla‐imidazolium salts and trapped by addition of transition‐metal complexes affording the corresponding heterodimetallic dicarbene derivatives, which can serve as carbene transfer agents.