Interstitial water and the formation of low barrier hydrogen bonds: A computational model study

The B3LYP/D95+(d,p) analysis of the uncharged low barrier hydrogen bond (LBHB) between 4‐methyl‐1H‐imidazole (Mim) and acetic acid (HAc) shows that uncharged LBHBs can be formed either by adding three water molecules around the cluster or by placing the Mim–HAc pair in a dielectric environment created by a polarizable continuum model with a permittivity larger than 20.7. The permittivity of environment around uncharged LBHB can be lowered significantly by including water molecules into the system. A Mim–HAc LBHB stabilized with one water molecule observed in diethyl ether (ε = 4.34), with two water molecules in toluene (ε = 2.38), and with three water molecules in vacuo (ε = 1). Solvation models with different numbers of water molecules predict average differences in the proton affinities of the hydrogen bonded bases (ΔPA) for stable uncharged LBHB systems in vacuo to be 91.5 kcal/mol being different from the ΔPA values close to zero in charge‐assisted LBHB systems. The results clearly indicate that small amounts of interstitial water molecules at the active site of enzymes do not preclude the existence of LBHBs in biological catalysis. Our results also show that interstitial water molecules provide a useful clue in the search for uncharged LBHBs in an enzymatic environment and the number of water molecules can be used as a relative measure for the polarity around the direct environment of LBHBs. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

DFT study on the hydrogen bonds of phenol–cyclohexanone and phenol–H2O2 in the Baeyer–Villiger oxidation

Hydrogen bonds of phenol–cyclohexanone and phenol–H₂O₂ in the studied Baeyer–Villiger (B–V) oxidation have been investigated by HF, B3LYP, and MP2 methods with various basis sets. The accurate single‐point energies were performed using CCSD(T)/6‐31+G(d,p) and CCSD(T)/aug‐cc‐pVDZ on the optimized geometries of MP2/6‐31+G(d,p). It has been confirmed that B3LYP/6‐31+G(d,p) could be used to study such hydrogen bonds. Energetic analysis of complexes was carried out using the Xantheas method with BSSE corrected by CP method. Orbital energy order (ε) illuminated that phenol with good hydrogen donor‐acceptor property can interact with cyclohexanone or H₂O₂ to form hydrogen bound complexes, and the binding energies (BE) range from ?4.38 to ?14.06 kcal mol^?1. NBO analysis indicated that the redistribution of atomic charges in the complexes facilitated nucleophilic attack of H₂O₂ on cyclohexanone. The calculated results match remarkably well with the experimental phenomena. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Direct ab‐initio molecular dynamics study on the radiation effects on catalytic triad composed of Ser‐His‐Glu residues

High energy irradiation to the hydrogen bonded system is important in relevance with the initial process of DNA and enzyme damages. In the present study, the effects of radiation to catalytic triad have been investigated by means of direct ab‐initio molecular dynamics (AIMD) calculation. As a model of the catalytic triad, Ser‐His‐Glu residue, which is one of the important enzymes in the acylation reaction, was examined. The ionization and electron attachment processes in Ser‐His‐Glu were investigated as the radiation effects. The direct AIMD calculation showed that a proton of His is spontaneously transferred to carbonyl oxygen of Glu after the ionization. However, the whole structure of catalytic triad was essentially kept after the ionization. On the other hand, in the case of the electron capture in the model catalytic triad Ser‐His‐Glu, the dissociation of Glu residue from [Ser‐His]^? was found as a product channel. The mechanism of ionization and electron capture process in the catalytic triad was discussed on the basis of theoretical results. © 2015 Wiley Periodicals, Inc.     

Hierarchical Organization of Ferrocene–Peptides

Hierarchical self‐assembly of disubstituted ferrocene (Fc)–peptide conjugates that possess Gly‐Val‐Phe and Gly‐Val‐Phe‐Phe peptide substituents leads to the formation of nano‐ and micro‐sized assemblies. Hydrogen‐bonding and hydrophobic interactions provide directionality to the assembly patterns. The self‐assembling behavior of these compounds was studied in solution by using ¹H NMR and circular dichroism (CD) spectroscopies. In the solid state, attenuated total reflectance (ATR) FTIR spectroscopy, single‐crystal X‐ray diffraction (XRD), powder X‐ray diffraction (PXRD), and scanning electron microscopy (SEM) methods were used. Spontaneous self‐assembly of Fc–peptides through intra‐ and intermolecular hydrogen‐bonding interactions induces supramolecular assemblies, which further associate and give rise to fibers, large fibrous crystals, and twisted ropes. In the case of Fc[CO‐Gly‐Val‐Phe‐OMe]₂ ( 1 ), molecules initially interact to form pleated sheets that undergo association into long fibers that form bundles and rectangular crystalline cuboids. Molecular offsets and defects, such as screw dislocations and solvent effects that occur during crystal growth, induce the formation of helical arrangements, ultimately leading to large twisted ropes. By contrast, the Fc–tetrapeptide conjugate Fc[CO‐Gly‐Val‐Phe‐Phe‐OMe]₂ ( 2 ) forms a network of nanofibers at the supramolecular level, presumably due to the additional hydrogen‐bonding and hydrophobic interactions that stem from the additional Phe residues.     

Comprehensive study of the interaction between hydrogen halides and methanol derivatives

The R? CH₂? HO…H? X (R = SCl, Cl, SH, NO₂, OMe, CHO, CN, C₂H₅, CH₃, H; X = F, Cl, Br) complexes are considered here as the interest sample for the consideration of different measures of H‐bond strength. The intermolecular interaction energies are predicted by using MP2/6‐31++G(d,p) and B3LYP/6‐31++G(d,p) methods with basis set superposition error and zero‐point energy corrections. The results showed that intermolecular hydrogen bonds for complexes with HF are stronger than such interactions in complexes with HCl and HBr. Quantum theory of “Atoms in Molecules” and natural bond orbitals method were applied to analyzed H‐bond interactions. The gas phase thermodynamic properties of complexes were predicted using quantum mechanical computations. The obtained results showed a strong influence of the R and X substituents on the thermodynamic properties of complexes. Numerous correlations between topological, geometrical, thermodynamic properties and energetic parameters were also found. © 2011 Wiley Periodicals, Inc.     

A theoretical study of the sulfenate–sulfoxide rearrangement. Effect of the hydrogen bond complexation

A DFT study of the thermal and radical sulfenate–sulfoxide rearrangement of derivatives of 3‐propenyl sulfoxide has been carried out. The effect of the substitution and hydrogen bond complexation has been analyzed. The results show that without external factors the radical breakdown path is the one preferred by the alkyl and aromatic derivatives while the unsubstituted system proceeds preferentially through a two‐step series of [1,3]‐ and [2,3]‐sigmatropic shifts. The inclusion of a hydrogen bond donor interacting with the oxygen atom increases the stability of all the species except the radical and the final products. Thus, in the dimethyl derivative the radical and two‐step processes present similar limiting steps. The analysis of the electron density of the systems provides some relationships between the properties at the bond critical point and the interatomic distances for the S···C and H···O cases. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2391–2397, 2010     

Theoretical investigation of gas phase ethanol–(water)n (n = 1–5) clusters and comparison with gas phase pure water clusters (water)n (n = 2–6)

Various properties (such as optimal structures, structural parameters, hydrogen bonds, natural bond orbital charge distributions, binding energies, electron densities at hydrogen bond critical points, cooperative effects, and so on) of gas phase ethanol–(water)_n (n = 1–5) clusters with the change in the number of water molecules have been systematically explored at the MP2/aug‐cc‐pVTZ//MP2/6‐311++G(d,p) computational level. The study of optimal structures shows that the most stable ethanol‐water heterodimer is the one where exists one primary hydrogen bond (O? H…O) and one secondary hydrogen bond (C? H …O) simultaneously. The cyclic geometric pattern formed by the primary hydrogen bonds, where all the molecules are proton acceptor and proton donor simultaneously, is the most stable configuration for ethanol–(water)_n (n = 2–4) clusters, and a transition from two‐dimensional cyclic to three‐dimensional structures occurs at n = 5. At the same time, the cluster stability seems to correlate with the number of primary hydrogen bonds, because the secondary hydrogen bond was extremely weaker than the primary hydrogen bond. Furthermore, the comparison of cooperative effects between ethanol–water clusters and gas phase pure water clusters has been analyzed from two aspects. First of all, for the cyclic structure, the cooperative effect in the former is slightly stronger than that of the latter with the increasing of water molecules. Second, for the ethanol–(water)₅ and (water)₆ structure, the cooperative effect in the former is also correspondingly stronger than that of the latter except for the ethanol–(water)₅ book structure. © 2012 Wiley Periodicals, Inc.     

Theoretical study of the Si–H group as potential hydrogen bond donor

The ability of the Si–H group as hydrogen bond (HB) donor has been studied theoretically. Most of the selected molecules include the Si–H group in a polar environment that could produce an electron deficiency on the hydrogen atom. In addition, analogous derivatives where the silicon atom has been replaced by a carbon atom have been considered. In all cases, ammonia has been used as HB acceptor. The calculations have been carried out at the MP2/6‐311++G** computational level. The electron density of the complexes has been characterized within the atoms in molecules (AIM) framework. A search in the Cambridge Structural Database (CSD) has been carried out to verify the existence of this kind of interactions in solid phase. The results of the theoretical study on these HB complexes between ammonia and the silicon derivatives provides long HB distances (2.4 to 3.2 Å) and small interaction energies (?2.4 to ?0.2 kcal/mol). In all cases, the HBs of the corresponding carbon analogs show shorter interaction distances corresponding to stronger complexes. The CSD search provides a small number of short interactions between Si and other heavy atoms in agreement with the small stabilizing energy of the Si–H?N HB and the lack of SiH bond in polar environment within the database. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

A Multi‐Center Energy Analysis of the Tunable Proton Affinity of Hydrogen Bonded Cluster Ions

The proton affinity (PA) of the [Tca–H^βMim]^? ion (Tca^?: trichloroacetate ion, HMim: 4‐Methyl‐1H‐imidazole) is a nearly linear function of the position (r₃) of H^β using the rigid framework approximation. This useful property of the ion is caused by an unusually large four‐center interaction term revealed by the multi‐center energy (MCE) analysis of PA(r₃). The MCE analysis shows further that despite the general stabilization of the [Tca–HMim–HAc]^? ion by cooperative effects, the individual hydrogen bonds carry a strong anti‐cooperative element caused by the rivalry of the two bases for the proton linking them.     

Direct NMR resonance assignments of the active site histidine residue in Escherichia coli thioesterase I/protease I/lysophospholipase L1

Owing to the hydrogen-bond interaction and rapid exchange rate with the bulk water, the transverse relaxation time for the N(delta1)-H proton of the catalytic histidine in Escherichia coli thioesterase I/protease I/lysophospholipase L1 (TEP-I) is rather short. Because of its catalytic importance, it is desirable to detect and assign this proton resonance. In this paper, we report the first direct NMR correlation between the short-lived N(delta1)-H proton and its covalently attached N(delta1)-nitrogen of the catalytic His157 residue in E. coli thioesterase/protease I. We have used gradient-enhanced jump-return spin-echo HMQC (GE-JR SE HMQC) to obtain a direct correlation between the short-lived N(delta1)-H proton and its covalently attached N(delta1)-nitrogen. The sensitivity of detection for the short-lived N(delta1)-H proton was enhanced substantially by improved water suppression, in particular, the suppression of radiation damping via pulsed field gradients.     

Computational Study on the Unconventional Hydrogen‐Bonded F–H···C Systems

The F–H···YZ₂ (Y = C, Si, BH, A1H;Z = H, PH₃) systems were examined using density functional theory calculations. The main focus of this work is to demonstrate that the chemistry of Y(PH₃)₂ exhibits a novel feature which is a central Y atom with unexpected high basicity. Further, the hydrogen bond strength can be adjusted by the substitution of H atoms of YH₂ by PH₃ groups. The FH···C(PH₃)₂ system has the strongest hydrogen bond interaction, which is larger than a conventional hydrogen bond. In addition to electrostatic interaction, donor‐acceptor interaction also plays an important role in determining the hydrogen bond strength. Therefore, a carbon atom can not only be the hydrogen bond acceptor but also can create an unusual stabilized hydrogen bond complex. Also, X₃B–YZ₂ (X = H, F; Y = C, Si, BH, A1H;Z = PH₃, NH₃) systems were examined, and it was found that the bond strength is controlled predominately by the HOMO‐LUMO gap (ΔIP). The smaller the ΔIP, the larger the bond dissociation energy of the B–Y bond. In addition, NH₃ is a better electron‐donating group than PH₃, and thus forms the strongest donor‐acceptor interaction between X₃B and Y(NH₃)₂.     

Site‐selective synthesis and characterization of BODIPY–acetylene copolymers and their transistor properties

To study the effect of site‐selective copolymerization of borondipyrromethene (BODIPY) with acetylene on the structural and optoelectronic properties, three copolymers P1–P3 were synthesized by the Sonogashira cross‐coupling of BODIPY units with diacetylene and bromine capping through all the possible linkages: α‐α ( P1 ), α‐β ( P2 ), and β‐β ( P3 ). The optoelectronic properties of the polymers were investigated systematically to understand the effect of site‐selective polymerization. The HOMO levels of the polymers were significantly tuned from P1 to P3 with negligible change in the LUMO levels. Broadening of absorption spectra from P3 to P1 was observed because of increase in the extent of conjugation. Additionally, the charge transport properties of these polymers in organic thin‐film transistors (OTFTs) revealed that P1 and P3 exhibited only p‐type mobility, whereas P2 exhibited electron mobility. Notably, the further investigations of the surface morphology of polymer films by atomic force microscopy (AFM) unveiled that comb like nanostructural arrangements in P3 was beneficial for the charge‐carrier mobility over the circular arrangements in P1 and P2 . © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 1978–1986     

Photoinduced Triplet–Triplet Energy Transfer in a 2‐Ureido‐4(1H)‐Pyrimidinone‐Bridged,Quadruply Hydrogen‐Bonded Ferrocene–Fullerene Assembly

2‐Ureido‐4(1H)‐pyrimidinone‐bridged ferrocene–fullerene assembly I is designed and synthesized for elaborating the photoinduced electron‐transfer processes in self‐complementary quadruply hydrogen‐bonded modules. Unexpectedly, steady‐state and time‐resolved spectroscopy reveal an inefficient electron‐transfer process from the ferrocene to the singlet or triplet excited state of the fullerene, although the electron‐transfer reactions are thermodynamically feasible. Instead, an effective intra‐assembly triplet–triplet energy‐transfer process is found to be operative in assembly I with a rate constant of 9.2×10⁵ s^?1 and an efficiency of 73 % in CH₂Cl₂ at room temperature.     

A Halogen‐Bonded Dimeric Resorcinarene Capsule

Iodine (I₂) acts as a bifunctional halogen‐bond donor connecting two macrocyclic molecules of the bowl‐shaped halogen‐bond acceptor, N‐cyclohexyl ammonium resorcinarene chloride 1 , to form the dimeric capsule [(1,4‐dioxane)₃@ 1 ₂(I₂)₂]. The dimeric capsule is constructed solely through halogen bonds and has a single cavity (V=511 ų) large enough to encapsulate three 1,4‐dioxane guest molecules.