P-O donor action from carboxylate anions with phosphorus in the presence of hydrogen bonding. A model for phosphoryl-transfer enzymes

A series of phosphorus compounds (1-3) containing anionic carboxylate groups were synthesized by treatment of the respective neutral precursor acid forms B-D with amines, which also served to introduce hydrogen-bonding interactions. The compounds, subjected to X-ray structure analysis, resulted in hexacoordinated anionic phosphoranates 1A and 1B, a pseudo-trigonal-bipyramidal anionic phosphine (2), and a trigonal-bipyramidal anionic phosphine oxide (3). The structures revealed that P-O donor coordination was present in all members of the anionic series 1-3 and resulted in stronger interactions than existed in the precursor neutral acid forms B-D as measured by the presence of shorter P-O distances. Evaluation of the energies of the donor interactions relative to the energies of the hydrogen bonds that were present showed that the donor energies now exceeded the hydrogen bond strengths. (31)P chemical shifts indicated that the basic coordination geometries were retained in solution. Both 1A and 1B are chiral and exist as racemates. The results suggest that mechanisms of phosphoryl-transfer enzymes should benefit by taking into account donor interactions at phosphorus by residues at active sites in addition to the inclusion of hydrogen bonding. Reference is made to specific phosphoryl-transfer enzymes.     

Pseudoheptacoordination and pseudohexacoordination in tris(2-N,N-dimethylbenzylamino)phosphane

The phosphane (C(6)H(4)-2-CH(2)NMe(2))(3)P (1) upon recrystallization from various solvents yielded the structurally different forms 1A, 1C, 1B(1), and 1B(2). Phosphane oxide (C(6)H(4)-2-CH(2)NOMe(2))(3)PO (2) was obtained from 1 by oxidation with hydrogen peroxide. X-ray analysis provided molecular structures for 1A, 1B(1), 1B(2), and 2. Phosphanes 1A and 1B(1) have pseudohexacoordinate frameworks as a result of the formation of two P-N donor interactions, 1B(2) has a pseudoheptacoordinate geometry due to the presence of three P-N interactions, and 2 resides in a tetrahedral geometry. The presence of the flexible dimethylaminobenzyl group in 1A, 1C, 1B(1), and 1B(2) is reasoned to be responsible for this variation in coordination geometry. Phosphane oxide 2 has very strong donor oxygen atoms from N-oxide groups but they are involved in competition with the presence of hydrogen bonding, which results in the lack of donor coordination. High-resolution (1)H, (13)C, and (31)P NMR measurements are also reported. The results provide evidence for the low-energy threshold required to allow hypercoordinated phosphorus to alter coordination geometry.     

Active Site Model for Phosphoryl Transfer Enzymes Via Hexacoordination

Previous work has demonstrated the ease with which phosphorus can increase its coordination geometry. The present study has more closely modeled active sites of phosphoryl transfer enzymes by the inclusion of anionic phosphorus, which allows for oxygen atom donor coordination at phosphorus in the presence of a hydrogen bonding network. The resulting increase in phosphorus-oxygen donor coordination compared to analogous systems containing neutral phosphorus compounds serves as a model applicable to proposed mechanisms at active sites of phosphoryl transfer enzymes.     

Phosphoryl Transfer Enzymes and Hypervalent Phosphorus Chemistry: A Keynote Lecture of the 7th International Conference on Heteroatom Chemistry

The coordination tendencies of phosphorus to form a hexacoordinated state from a pentacoordinated state which might assist in describing mechanistic action of phosphoryl transfer enzymes are delineated. The factors discussed include substrate and transition or intermediate state anionicity; hydrogen bonding; packing effects, i.e., van der Waals forces; the ease of formation of hexacoordinate phosphorus from lower coordinate states; and the pseudorotation problem common to nonrigid pentacoordinate phosphorus. In view of the work reported in this account and recent work on enzyme promiscuity and moonlighting activities, it is suggested that donor action should play a role in determining active-site interactions in phosphoryl transfer enzyme mechanisms.     

Refined models for the preferential interactions of tryptophan with phosphocholines

A series of molecular models of the adducts formed between N-acetyl-l-tryptophan ethylamide and diacetyl-sn-glycero-3-phosphocholine have been generated. Using rOesy data that enabled us to place restrictions on the proximity of a number of key protons in the amino acid/phosphocholine pairs, a series of structures were generated following molecular dynamics and mechanics experiments using the CHARMM27 force field. These structures were then subjected to a series of clustering algorithms in order to classify the tight binding interactions between a single tryptophan and a phosphocholine. From these analyses, it is evident that: (i) binding is characterised by hydrogen bonding between the indole NH as donor and phosphate oxygen as acceptor, cation-carbonyl interactions between the choline ammonium and amide carbonyl groups and cation-pi interactions; (ii) cation-pi interactions are not always observed, particularly when their formation is at the expense of cation-carbonyl and hydrogen bonding interactions; (iii) on the basis of amino acid torsional parameters, it is possible to predict whether the phosphocholine headgroup will bind in a compact or elongated conformation. Extension of the procedures to characterise 2 : 1 Trp-PC binding revealed that the same intermolecular interactions are predominant; however, combinations of all three intermolecular interactions within the same adduct occur much more frequently due to the availability of donor/acceptor groups from both tryptophans in the 2 : 1 system.     

无机化学中空间效应的定量研究——Ⅱ、分子结构在成键前的几何框架

本文提出分子结构在成键前的几何框架概念。根据座位—配体匹配方法计算四体配位型分子的几何框架,并与实测结构对比,结果相近,表明在弱轨道作用下,配体的大小是决定分子构型的主要因素。同时讨论了引起几何框架扭曲的原因。     

Hydrogen-bond-directing effect in the ionothermal synthesis of metal coordination polymers

Four new cobalt coordination polymers, (EMIm)[Co2(TMA-H)2(44bpy)3]Br 1, (EMIm)[Co(TMA-H)(44bpy)2](44bpy)Br 2, (EMIm)[Co(TMA)(Im-H)]3 and (EMIm)2[Co(TMA)2(TED-H2)] 4, were prepared from 1-ethyl-3-methyl imidazolium bromide (EMIm-Br). All the compounds have similar two-dimensional cobalt trimesate (TMA) coordination layers but different three-dimensional supramolecular architectures that contain one of three potentially ditopic amines, 4,4'-bipyridine (44bpy), imidazole (Im-H) and triethylenediamine (TED). Two-fold interpenetration of hydrogen-bonding networks was found for 1, 2 and 4. The coordination layers of 1 and 2 are neutral while 3 and 4 have anionic molecular assemblies. The use of organic amines, that act as supramolecular bridging ligands, introduces hydrogen-bond-directing effects in the ionothermal synthesis of metal coordination polymers. Hydrogen bonding helps to align the packing between the coordination layers and control the formation of 3D supramolecular networks. In 1, hydrogen bonds between the ionic species within the channels direct the alignment of non-directional electrostatic interactions between EMIm+ and Br(-) ions, which is a rare case of a hydrogen-bond-templating effect of ionic liquids in ionothermal synthesis.     

Simulations of liquid ammonia based on the combined quantum mechanical/molecular mechanical (QM/MM) approach

Two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely, HF/MM and B3LYP/MM, have been performed to investigate the local structure and dynamics of liquid ammonia. The most interesting region, a sphere containing a central reference molecule and all its nearest surrounding molecules (first coordination shell), was treated by the Hartree-Fock (HF) and hybrid density functional B3LYP methods, whereas the rest of the system was described by the classical pair potentials. On the basis of both HF and B3LYP methods, it is observed that the hydrogen bonding in this peculiar liquid is weak. The structure and dynamics of this liquid are suggested to be determined by the steric packing effects, rather than by the directional hydrogen bonding interactions. Compared to previous empirical as well as Car-Parrinello (CP) molecular dynamics studies, our QM/MM simulations provide detailed information that is in better agreement with experimental data.     

Hydrolysis of 2',3'-O-methyleneadenosin-5'-yl bis-5'-O-methyluridin-3'-yl phosphate: the 2'-hydroxy group stabilizes the phosphorane intermediate, not the departing 3'-oxyanion, by hydrogen bonding

Hydrolytic reactions of 2',3'-O-methyleneadenosin-5'-yl bis-5'-O-methyluridin-3'-yl phosphate (1a) have been followed by RP HPLC over a wide pH range to elucidate the role of the 2'-OH group as an intermolecular hydrogen bond donor facilitating the cleavage of 1a. At pH < 2, where the decomposition of 1 is first-order in hydronium-ion concentration, the P-O5' and P-O3' bonds are cleaved equally rapidly. Over a relatively wide range from pH 2 to 4, the hydrolysis is pH-independent and the P-O5' bond is cleaved 1.6 times as rapidly as the P-O3' bond. At pH 6, the reaction becomes first-order in hydroxide-ion concentration and cleavage of the P-O3' bond starts to predominate, accounting for 89% of the overall hydrolysis in 10 mmol L(-)(1) aqueous sodium hydroxide. Under alkaline conditions, the 2'-OH group facilitates the cleavage of 1 by a factor of 27 compared to the 2'-OMe counterpart, the influence on the P-O3' and P-O5' bond cleavage being equal. Accordingly, the 2'-hydroxy group stabilizes the phosphorane intermediate, not the departing 3'-oxyanion, by hydrogen bonding.     

Structural criteria for the rational design of selective ligands: convergent hydrogen bonding sites for the nitrate anion

A large number of crystal structures are analyzed to characterize the structural aspects of hydrogen bonding interactions with the NO(3)(-) anion. Further insight is provided by the use of electronic structure calculations to determine stable geometries and interaction energies for NO(3)(-) complexes with several simple hydrogen bond donor groups, including water, methanol, N-methylform-amide, and methane. The results establish the existence of a clear set of structural criteria for the rational design of molecular receptors that complex the NO(3)(-) anion through hydrogen bonding interactions.     

The hydrogen bonding properties of cytosine: a computational study of cytosine complexed with hydrogen fluoride, water, and ammonia

Density functional theory is used to study the hydrogen bonding pattern in cytosine, which does not contain alternating proton donor and acceptor sites and therefore is unique compared with the other pyrimidines. Complexes between various small molecules (HF, H(2)O, and NH(3)) and four main binding sites in (neutral and (N1) anionic) cytosine are considered. Two complexes (O2(N1) and N3(N4)) involve neighboring cytosine proton acceptor and donor sites, which leads to cooperative interactions and bidendate hydrogen bonds. The third (less stable) complex (N4) involves a single cytosine donor. The final (O2-N3) complex involves two cytosine proton acceptors, which leads to an anticooperative hydrogen bonding pattern for H(2)O and NH(3). On the neutral surface, the anticooperative O2-N3 complex is less stable than those involving bidentate hydrogen bonds, and the H(2)O complex cannot be characterized when diffuse functions are included in the (6-31G(d,p)) basis set. On the contrary, the anionic O2-N3 structure is the most stable complex, while the HF and H(2)O N3(N4) complexes cannot be characterized with diffuse functions. B3LYP and MP2 potential energy surface scans are used to consider the relationship between the water N3(N4) and O2-N3 complexes. These calculations reveal that diffuse functions reduce the conversion barrier between the two complexes on both the neutral and anionic surfaces, where the reduction leads to a (O2-N3) energy plateau on the neutral surface and complete (N3(N4)) complex destabilization on the anionic surface. From these complexes, the effects of hydrogen bonds on the (N1) acidity of cytosine are determined, and it is found that the trends in the effects of hydrogen bonds on the (N1) acidity are similar for all pyrimidines.     

Influence of <Emphasis Type="Italic">gauche</Emphasis> effect on uncharged oxime reactivators for the reactivation of tabun-inhibited AChE: quantum chemical and steered molecular dynamics studies

The neutral oxime reactivator RS194B with a seven-membered ring has shown better efficacy towards the tabun-inhibited AChE than that of RS69N with a six-membered ring and RS41A with a five-membered ring. The difference in the efficacy of these reactivators has remained unexplored. We report here the origin of the difference of efficacy of these reactivators based on the conformational analysis, quantum chemical calculations and steered molecular dynamics (SMD) simulations. The conformational analysis using B3LYP/6-31G(d) level of theory revealed that RS41A and RS194B are more stable in gauche conformation due to the gauche effect (–N–C–C–N– bonds) whereas RS69N prefers anti-conformation. The SMD simulations show that RS194B retains in more stable gauche conformation inside the active gorge of AChE during different time intervals that experiences more hydrogen bonding, hydrophobic interactions with the catalytic anionic site (CAS) residues and weaker interactions with the peripheral anionic site (PAS) residues compared to RS41A and RS69N. In an effort to design an even superior reactivator, RS194B-S has been chosen with a subtle change in the geometry of RS194B by replacing the carbonyl oxygen with the sulfur atom. The newly designed reactivator RS194B-S can also be a promising candidate to reactivate tabun-inhibited AChE.     

Engineering Crystals Using sp3-C Centred Tetrel Bonding Interactions

1,1,2,2-Tetracyanocyclopropane derivatives 1 and 2 were designed and synthesized to probe the utility of sp³-C centred tetrel bonding interactions in crystal engineering. The crystal packing of 1 and 2 and their 1,4-dioxane cocrystals is dominated by sp³-C(CN)₂⋅⋅⋅O interactions, has significant C⋅⋅⋅O van der Waals overlap (≤0.266 Å) and DFT calculations indicate interaction energies of up to −11.0 kcal mol⁻¹. A cocrystal of 2 with 1,4-thioxane reveals that the cyclopropane synthon prefers interacting with O over S. Computational analyses revealed that the electropositive C₂(CN)₄ pocket in 1 and 2 can be seen as a strongly directional ‘tetrel-bond donor’, similar to halogen bond or hydrogen bond donors. This disclosure is expected to have implications for the utility of such ‘tetrel bond donors’ in molecular disciplines such as crystal engineering, supramolecular chemistry, molecular recognition and medicinal chemistry.     

Heterometallic FeIII/K Coordination Polymer with a Wide Thermal Hysteretic Spin Transition at Room Temperature

The anionic Fe^III complex exhibiting cooperative spin transition with a wide thermal hysteresis near room temperature, K[Fe(5‐Brthsa)₂] (5‐Brthsa‐H₂=5‐bromosalicylaldehyde thiosemicarbazone), is reported. The hysteresis (Δ=69 K in the first cycle) shows a one‐step transition in heating mode and a two‐step transition in cooling mode. X‐ray structure analysis showed that the coexistence of hydrogen bond and cation–π interactions, as well as alkali metal coordination bonds, to give 2D coordination polymer structure. This result is contrary to previous reports of broad thermal hysteresis induced by coordination bonds of Fe^II spin crossover coordination polymers (with 1D/3D structures), and by strong intermolecular interactions in the molecular packing through π–π stacking or hydrogen‐bond networks. As a consequence, the importance, or the very good suitability of alkali metal‐based coordination bonds and cation–π interactions for communicating cooperative interactions in spin‐crossover (SCO) compounds must be reconsidered.     

A new 1D coordination polymer constructed by CaCl2 with 5-aminoiosphtalic acid (H2AIP) and 1,10-phenanthroline ligands using the water bath method

A new coordination polymer, [Ca(AIP)(Phen)(H₂O)₂] · Phen · H₂O (H₂AIP = 5-aminoisophthalic acid, Phen = 1,10-phenanthroline), was synthesized using the water bath method and characterized by elemental analyses and single crystal X-ray diffraction, which revealed that I has an interesting 1D chain structure. The adjacent chains are further connected together via the π-π packing interactions and hydrogen bonding interactions.     

How well can density functional methods describe hydrogen bonds to pi acceptors?

We employed four newly developed density functional theory (DFT) methods for the calculation of five pi hydrogen bonding systems, namely, H2O-C6H6, NH3-C6H6, HCl-C6H6, H2O-indole, and H2O-methylindole. We report new coupled cluster calculations for HCl-C6H6 that support the experimental results of Gotch and Zwier. Using the best available theoretical and experimental results for all five systems, our calculations show that the recently proposed MPW1B95, MPWB1K, PW6B95, and PWB6K methods give accurate energetic and geometrical predictions for pi hydrogen bonding interactions, for which B3LYP fails and PW91 is less accurate. We recommend the most recent DFT method, PWB6K, for investigating larger pi hydrogen bonded systems, such as those that occur in molecular recognition, protein folding, and crystal packing.     

Insights into metal borohydride and aluminohydride bonding: X-ray and neutron diffraction structures and a DFT and charge density study of [Na(15-crown-5)][EH(4)] (E = B, Al)

The neutron and X-ray structures of [Na(15-crown-5)][BH(4)] and [Na(15-crown-5)][AlH(4)], respectively, are reported, along with a topological analysis of their DFT-computed charge densities that explores the bonding between the anionic complex hydride [EH(4)](-) (E = B, Al) and the counterion [Na(15-crown-5)](+). In each case, the interaction is weak and mainly electrostatic in nature; however, notable differences are observed in the manner in which [BH(4)](-) and [AlH(4)](-) bind to the metal, which explains their different coordination modes. A range of unconventional E-H···H-C contacts is revealed to play an important role in the overall bonding and crystal packing of both complexes. These interactions can be classified as weak dihydrogen bonds based on the atoms in molecules approach.     

Modeling anhydrous and aqua copper(II) amino acid complexes: a new molecular mechanics force field parametrization based on quantum chemical studies and experimental crystal data

This paper presents the vacuum structures of aquacopper(II) bis(amino acid) complexes with glycine, sarcosine, N,N-dimethylglycine, and N-tert-butyl-N-methylglycine estimated using the B3LYP method. The differences between the B3LYP vacuum structures and experimental crystal structures suggested considerable influence of crystal lattice packing effects on the changes in the complexes' geometries. A previously developed molecular mechanics force field for modeling anhydrous copper(II) amino acidates was reoptimized to simulate these changes and predict the properties of both trans and cis anhydrous and aqua copper(II) amino acid complexes. The modeling included experimental molecular and crystal structures of 13 anhydrous and 10 aqua copper(II) amino acidates with the same atom types (Cu(II), C, H, N, and O) but various copper(II) coordination polyhedron geometries, crystal symmetries, and intermolecular interactions. The empirical parameters of the selected potential energy functions were optimized on the B3LYP vacuum copper(II) coordination geometries of three anhydrous copper(II) amino acidates and on experimental crystalline internal coordinates and unit cell dimensions of six anhydrous and six aqua copper(II) amino acid complexes. The respective equilibrium structures were calculated in vacuo and in simulated crystalline environment. The efficacy of the final force field, FFW, was examined. The total root-mean-square deviations between the experimental and theoretical crystal values were 0.018 A in the bond lengths, 2.2 degrees in the valence angles, 5.5 degrees in the torsion angles, and 0.395 A in the unit cell lengths. FFW reproduced the unit cell volumes in the range from -8.1 to 9.6%. The means of Cu to axial water oxygen distances were 2.4 +/- 0.1 A (experiment) and 2.6 +/- 0.1 A (FFW). This paper describes the ability of the molecular mechanics model and FFW force field to simulate the flexibility of the metal coordination polyhedron. The new force field proved effective in predicting the most stable molecular conformation of copper(II) amino acidato systems in vacuo.     

First systematic investigation of C-H...Cl hydrogen bonding using inorganic supramolecular synthons: lamellar, stitched stair-case, linked-ladder, and helical structures

Using a group of six neutral M(II)Cl(2)-containing coordination compounds as building blocks, the first systematic investigation of C-H...Cl hydrogen-bonding interactions was performed. Single-crystal X-ray structural analyses of four new compounds (pseudo-tetrahedral Co(II) and Zn(II); distorted trigonal bipyramidal Zn(II)) authenticate the metal coordination geometry. To provide a unified view of the presence of noncovalent interactions in this class of compounds, we have re-examined the packing diagram of two previously reported compounds (a distorted square-pyramidal Cu(II) complex and a trans-octahedral Co(II) complex). The organic ligands of our choice comprise bidentate/tridentate pyrazolylmethylpyridines and an unsymmetrical tridentate pyridylalkylamine. This systematic investigation has allowed us to demonstrate the existence of versatile C-H...Cl(2)M interactions and to report the successful application of such units as inorganic supramolecular synthons. Additional noncovalent interactions such as C-H...O and O-H...Cl hydrogen bonding and pi-pi stacking interactions have also been identified. Formation of novel supramolecular architectures has been revealed: 2D lamellar (p-cyclophane) and 3D lamellar, 3D "stitched staircase" (due to additional hydrogen-bonding interactions by water tetramers, with an average O-O bond length in the tetramer unit of 2.926 A, acting as "molecular clips" between staircases), 3D linked ladder, and single-stranded 1D helix.     

An examination of intermolecular and intramolecular hydrogen bonding in biomolecules by AM1 and MNDO/M semiempirical molecular orbital studies

The recent NMDO/M modification and parameterization of the MNDO molecular orbital method has been used to analyze intermolecular hydrogen bonding between amino acids and water, and intramolecular hydrogen bonding in monosaccharides. The results have been compared to AM1 calculations on the same systems. The MNDO/M calculations gave values which were similar to ab initio calculations with respect to the intermolecular interactions, but yielded significantly poorer results for the intramolecular interactions. The AM1 procedure performed better on the intramolecular interactions than the MNDO/M procedure, but frequently provided unfavorable three-centered hydrogen bonding geometries for the intermolecular interactions.