Total synthesis and evaluation of [Psi[CH2NH]Tpg4]vancomycin aglycon: reengineering vancomycin for dual D-Ala-D-Ala and D-Ala-D-Lac binding

An effective synthesis of [Psi[CH(2)NH]Tpg(4)]vancomycin aglycon (5) is detailed in which the residue 4 amide carbonyl of vancomycin aglycon has been replaced with a methylene. This removal of a single atom was conducted to enhance binding to D-Ala-D-Lac, countering resistance endowed to bacteria that remodel their D-Ala-D-Ala peptidoglycan cell wall precursor by a similar single atom change (ester O for amide NH). Key elements of the approach include a synthesis of the modified vancomycin ABCD ring system featuring a reductive amination coupling of residues 4 and 5 for installation of the deep-seated amide modification, the first of two diaryl ether closures for formation of the modified CD ring system (76%, 2.5-3:1 kinetic atropodiastereoselectivity), a Suzuki coupling for installation of the hindered AB biaryl bond (90%) on which the atropisomer stereochemistry could be thermally adjusted, and a macrolactamization closure of the AB ring system (70%). Subsequent DE ring system introduction enlisted a room-temperature aromatic nucleophilic substitution reaction for formation of the remaining diaryl ether (86%, 6-7:1 kinetic atropodiastereoselectivity), completing the carbon skeleton of 5. Consistent with expectations and relative to the vancomycin aglycon, 5 exhibited a 40-fold increase in affinity for D-Ala-D-Lac (K(a) = 5.2 x 10(3) M(-1)) and a 35-fold reduction in affinity for D-Ala-D-Ala (K(a) = 4.8 x 10(3) M(-1)), providing a glycopeptide analogue with balanced, dual binding characteristics. Beautifully, 5 exhibited antimicrobial activity (MIC = 31 microg/mL) against a VanA-resistant organism that remodels its D-Ala-D-Ala cell wall precursor to d-Ala-d-Lac upon glycopeptide antibiotic challenge, displaying a potency that reflects these binding characteristics.     

Partitioning schemes for the 2-matrix and the pair density

Several schemes are discussed for partitioning the second-order reduced density matrix Γ into two parts, Γ⁰ and Γ′. The Γ⁰s are based on the independent particle model and the Γ′s are corrections due to electron correlation. The difficulties of choosing a Γ⁰ that will serve as a suitable reference point for studying electron correlation are discussed. In order to compare alternative partitioning schemes, an atomic wave function for the ¹S ground state of the Be atom in the configuration-interaction approximation was selected. A fifty-two configuration wave function was computed and contour graphs were made of the total pair density Γ(1 2) and of the “correlation pair density” Γ′(1 2) for several choices of the reference Γ⁰.     

Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems

In several previous studies, we performed sensitivity analysis to gauge the relative importance of different atomic partial charges in determining protein-ligand binding. In this work, we gain further insights by decomposing these results into three contributions: desolvation, intramolecular interactions, and intermolecular interactions, again based on a Poisson continuum electrostatics model. Three protein kinase-inhibitor systems have been analyzed: CDK2-deschloroflavopiridol, PKA-PKI, and LCK-PP2. Although our results point out the importance of specific intermolecular interactions to the binding affinity, they also reveal the remarkable contributions from the solvent-mediated intramolecular interactions in some cases. Thus, it is necessary to look beyond analyzing protein-ligand interactions to understand protein-ligand recognition or to gain insights into designing ligands and proteins. In analyzing the contributions of the three components to the overall binding free energy, the PKA-PKI system with a much larger ligand was found to behave differently from the other two systems with smaller ligands. In the former case, the intermolecular interactions are very favorable, and together with the favorable solvent-mediated intramolecular interactions, they overcome the large desolvation penalties to give a favorable electrostatics contribution to the overall binding affinity. On the other hand, the other two systems with smaller ligands only present modest intermolecular interactions and they are not or are only barely sufficient to overcome the desolvation penalty even with the aid of the favorable intramolecular contributions. As a result, the binding affinity of these two systems do not or only barely benefit from electrostatics contributions.     

Phase transition in Tl2TeO3: influence and origin of the thallium lone pair distortion

A new modification of thallium tellurite, beta-Tl(2)TeO(3), has been synthesized by methanolothermal reaction, and its phase transition has been studied by single-crystal X-ray diffraction. At a temperature of 440(10) degrees C an irreversible phase transition from a monoclinic structure (beta-Tl(2)TeO(3): P2(1)/c (No. 14), Z = 4, a = 8.9752(18) A, b = 4.8534(6) A, c = 11.884(2) A, beta = 109.67(2) degrees, V = 487.47(15) A3 at 25 degrees C) to an orthorhombic structure (alpha-Tl(2)TeO(3): Pban (No. 50), Z = 8, a = 16.646(2) A, b = 11.094(2) A, c = 5.2417(8) A, V = 968.0(3) A3 at 25 degrees C) is observed. Both structures are characterized by psi-tetrahedral TeO(3)(2-) anions. In the orthorhombic structure psi-trigonal bipyramidal [TlO(4)] units are found together with psi-tetrahedral [TlO(3)] units whereas in the monoclinic structure the coordination polyhedron around Tl(I) can be best described as a psi-square pyramide, psi-[TlO(4)]. The electronic structure of Tl(2)TeO(3) in both modifications has been studied to explain the influence of the lone pairs. It can be conclusively shown that the minimization of antibonding ns-metal/2p-oxygen interactions is the driving force for "lone pair" distortions which determines the structures of Tl(2)TeO(3).     

Reactions of coordinated hydroxymethylphosphines with NH-functional amines: the phosphorus lone pair is crucial for the phosphorus Mannich reaction

Non-coordinated hydroxymethylphosphines react readily with primary and secondary amines by the phosphorus Mannich reaction. To determine if this reactivity can be used to synthesize phosphine macrocycles, trans-Fe(DHMPE)(2)Cl(2) (DHMPE = 1,2-bis(dihydroxymethylphosphino)ethane) was prepared and reacted with various amines. However, no phosphorus Mannich reactivity was observed. In order to understand why no reactions occurred, the Mannich reactivity of the borane-coordinated hydroxymethylphosphines DHMPE·2BH(3) and Ph(2)PCH(2)OH·BH(3) was investigated. These borane-coordinated phosphines also did not undergo the phosphorus Mannich reaction. These results suggest that the lone pair of electrons on the phosphorus atom is essential for the phosphorus Mannich reaction to occur, and therefore it is not possible to use this reaction in a templated synthesis of phosphine macrocycles. It is speculated that the mechanism of the phosphorus Mannich reaction may involve a methylenephosphonium intermediate, analogous to an iminium in the standard Mannich reaction. X-ray crystal structures of trans-Fe(DHMPE)(2)Cl(2) and DHMPE·2BH(3) are also presented. Both crystal structures display an extended hydrogen-bonding network in the solid state.     

The stability and eventual lone pair distortion of the hexahalide complexes and molecules of the fifth to eighth main-group elements with one lone pair, as isolated entities or in oligomeric clusters: a vibronic coupling and DFT study

The introduced DFT-supported vibronic coupling model together with the hardness rule indicates, for the title compounds, that the tendency toward lone pair (LP) distortions decreases with increasing coordination number (CN) and upon proceeding from fluoride to iodide as the ligands. Thus, only some hexafluoro complexes and molecules are calculated to actually undergo LP deformations; here, from the possible highest-symmetry deformations, those with C(4v) geometry possess the lowest energy, leading to the complete ablation of one ligand and, hence, explaining the nonexistence of the complexes AsF6(3-), SbF6(3-), and SF6(2-). If a lower-symmetry strain is imposed on the octahedral species, for example, induced by the simultaneous presence of terminal and bridging ligands in oligomers, the vibronic energy potential is activated. It may induce pronounced distortions, which are much larger than those of analogous clusters with central ions lacking the LP. Dimers and tetramers with common edges and faces are investigated, with the predicted and calculated deformations of the constituting octahedra again following the stability sequence C(4v) > C(2v) > C(3v). The model nicely accounts for the observed trends, as well as reproduces the experimental structures and energy balances, at least semiquantitatively; its predictive power exceeds that of the valence-shell electron-pair repulsion concept.     

Theoretical investigation of lone pair inversions, ring openings, and hydride shifts in O-methylated epoxides

Mechanisms associated with the isomerization of the O-methylethylene oxonium ion and its tetramethyl-substituted analogue have been explored using correlated electronic structure calculations. The minima and transition states associated with inversion at the oxygen atom, as well as those associated with opening of the epoxide ring, have been characterized. The calculated barrier to inversion at the oxygen atom for the O-methylethylene oxonium ion, 15.7 kcal/mol, agrees well with the experimentally determined value, 10+/-2 kcal/mol. Our calculations indicate that a significantly higher barrier exists for the ring-opening mechanism that leads to more thermodynamically stable structures. This work includes the first known calculations on the O-methyl-2,3-dimethyl-2-butene oxonium ion along with transition states and intermediates associated with ring opening and inversion at the oxygen atom. Results show that there is a significantly lower barrier to ring opening as compared to the O-methylethylene oxonium ion species, leading to a lower probability of isolating this species. The effects of basis sets and correlation techniques on these ions were also analyzed in this work. Our results indicate that the B3LYP/6-31G* level is reliable for obtaining molecular geometries for both minima and transition states on the C3H7O+ and C7H15O+ potential energy surfaces.     

Non-specific binding in the affinity chromatography of chymotrypsin

The strong and specific binding of chymotrypsin on chromatographic columns containing agarose substituted with N--amino Caproyl- -tryptophan methyl ester is abolished when the -amino groups on the surface of the enzyme are reacted with acetic anhydride. Because the catalytic properties of the acetylated chymotrypsin are identical to those of the underivatized enzyme, it is concluded that the high affinity of chymotrypsin for this column is not due solely to biospecific inhibitor binding, which is by itself very weak, but requires reinforcement through weak non-specific interactions with the column support. It is postulated that these non-specific interactions include electrostatic interactions between agarose matrix and positively charged lysyl residues on the enzyme. The results demonstrate for the first time that residues on the surface of an enzyme not associated with its active site can play an important role in some chromatographic systems previously thought to be based on purely biospecific interactions.     

Influence of the anion on lone pair formation in Sn(II) monochalcogenides: a DFT study

The electronic structure of SnO, SnS, SnSe, and SnTe in the rocksalt, litharge, and herzenbergite structures has been calculated using density functional theory. Comparison of the distorted and undistorted structures allows for an explanation of the unusual experimentally observed structural transitions seen along the Sn(II) monochalcogenides. Analysis of the electronic structure shows a strong anion dependence of the Sn(II) lone pair, with the Sn(5s) and Sn(5p) states too far apart to couple directly. However, the interaction of Sn(5s) with anion states of appropriate energy produce a filled antibonding Sn(5s)-anion p combination which allows coupling of Sn(5s) and Sn(5p) to occur, resulting in a sterically active asymmetric density on Sn. While the interaction between Sn(5s) and O(2p) is strong, interactions of Sn with S, Se, and Te become gradually weaker, resulting in less high energy 5s states and hence weaker lone pairs. The stability of the distorted structures relative to the symmetric structures of higher coordination is thereby reduced, which induces the change from highly distorted litharge SnO to highly symmetric rocksalt SnTe seen along the series.     

Assignment of the four lowest ionized states of p-benzoquinone and the question of “lone pair splitting” in this system

The lowest ionized states of p-benzoquinone are assigned to be n_/²B_3g, n₄/²B_2u, π₁/²B_3u, and π₂/²B_1g in order of increasing energy. This sequence of states confirms Turner's original assignment and invalidates subsequent proposals. The origin of the difficulties with these assignments are traced back to the non-validity of Koopmans' theorem for the “oxygen lone pair” ionizations (i.e., ionization to the n_/²B_3g and n₊/²B_2u states).     

Electron affinity of the guanine-cytosine base pair and structural perturbations upon anion formation

The adiabatic electron affinity (AEA) for the Watson-Crick guanine-cytosine (GC) DNA base pair is predicted using a range of density functional methods with double- and triple-zeta plus polarization plus diffuse (DZP++ and TZ2P++) basis sets in an effort to bracket the true electron affinity. The methods used have been calibrated against a comprehensive tabulation of experimental electron affinities (Chem.Rev. 2002, 102, 231). Optimized structures for GC and the GC anion are compared to the neutral and anionic forms of the individual bases as well as Rich's 1976 X-ray structure for sodium guanylyl-3',5'-cytidine nonahydrate, GpC.9H(2)O. Structural distortions and natural population (NPA) charge distributions of the GC anion indicate that the unpaired electron is localized primarily on the cytosine moiety. Unlike treatments using second-order perturbation theory (MP2), density functional theory consistently predicts a substantial positive adiabatic electron affinity for the GC pair (e.g., TZ2P++/B3LYP: +0.48 eV). The stabilization of C(-) via three hydrogen bonds to guanine is sufficient to facilitate adiabatic binding of an electron to GC and is also consistent with the positive experimental electron affinities obtained by photoelectron spectroscopy of cytosine anions incrementally microsolvated with water molecules. The pairing (dissociation) energy for GC(-) (35.6 kcal/mol) is determined with inclusion of electron correlation and shows the anion to have greater thermodynamic stability; the pairing energy for neutral GC (TZ2P++/B3LYP 23.9 kcal/mol) compares favorably to previous MP2/6-31G (23.4 kcal/mol) results and a debated experiment (21.0 kcal/mol).     

The importance of lone pair delocalizations: theoretical investigations on the stability of cis and trans isomers in 1,2-halodiazenes

The relative and thermodynamic stabilities of cis and trans isomers of 1,2-dihalodiazenes (XN=NX; X = F, Cl, or Br) were examined using high level ab initio and density functional theory (DFT) calculations. For 1,2-dihalodiazenes, it was found that the cis isomers were more stable than the corresponding trans isomers, despite the existence of several cis destabilizing mechanisms, such as steric exchange between halogen lone pairs and dipole-dipole electrostatic repulsions (Delta(trans-cis) = 3.15, 7.04, and 8.19 kcal mol(-1), respectively, at BP86/6-311++G(3df,3pd)//B3LYP /6-311++G(3df,3pd) level). Their origin of the cis-preferred difference in energy was investigated with natural bond orbital (NBO) analysis to show that the "cis effect" came mainly from antiperiplanar interactions (AP effect) between the nitrogen lone pair and the neighboring antibonding orbital of the N-X bond (n(N) --> sigma(N'X'*)). The delocalization of halogen lone-pair into the antibonding orbital of the N=N bonds (the LP effects) was also found to enhance the cis preference by 1.20 to 6.58 kcal mol(-1), depending on the substituted halogen atom. The total amount of the AP effect increased as the halogen atom became larger, and the increased AP effect promoted the triple-bond-like nature of the N=N bond (shorter N=N bond length and wider NNX angle). The greater AP effect also made the N'-X' bond easier to cleave (longer N-X bond length), and a higher energy level than that of the nitrogen lone pair was found in the N-Br bonding orbital in 1,2-dibromodiazenes, thus indicating the significant instability of this molecule. The degradability of the N-Cl bond in 1,2-dichlorodiazenes and the fair stability of the N-F bond in 1,2-fluorodiazenes were also confirmed theoretically, and were found to be consistent with the previous experimental and theoretical reports. These results clearly indicate the dominance of lone-pair-related hyperconjugations on the basic electronic structure and energetic natures of 1,2-dihalodiazene systems.     

Structure-based approach for the study of estrogen receptor binding affinity and subtype selectivity

Estrogens exert important physiological effects through the modulation of two human estrogen receptor (hER) subtypes, alpha (hERalpha) and beta (hERbeta). Because the levels and relative proportion of hERalpha and hERbeta differ significantly in different target cells, selective hER ligands could target specific tissues or pathways regulated by one receptor subtype without affecting the other. To understand the structural and chemical basis by which small molecule modulators are able to discriminate between the two subtypes, we have applied three-dimensional target-based approaches employing a series of potent hER-ligands. Comparative molecular field analysis (CoMFA) studies were applied to a data set of 81 hER modulators, for which binding affinity values were collected for both hERalpha and hERbeta. Significant statistical coefficients were obtained (hERalpha, q(2) = 0.76; hERbeta, q(2) = 0.70), indicating the internal consistency of the models. The generated models were validated using external test sets, and the predicted values were in good agreement with the experimental results. Five hER crystal structures were used in GRID/PCA investigations to generate molecular interaction fields (MIF) maps. hERalpha and hERbeta were separated using one factor. The resulting 3D information was integrated with the aim of revealing the most relevant structural features involved in hER subtype selectivity. The final QSAR and GRID/PCA models and the information gathered from 3D contour maps should be useful for the design of novel hER modulators with improved selectivity.     

Quantitative study of interactions between oxygen lone pair and aromatic rings: substituent effect and the importance of closeness of contact

Current models describe aromatic rings as polar groups based on the fact that benzene and hexafluorobenzene are known to have large and permanent quadrupole moments. This report describes a quantitative study of the interactions between oxygen lone pair and aromatic rings. We found that even electron-rich aromatic rings and oxygen lone pairs exhibit attractive interactions. Free energies of interactions are determined using the triptycene scaffold and the equilibrium constants were determined by low-temperature 1H NMR spectroscopy. An X-ray structure analysis for one of the model compounds confirms the close proximity between the oxygen and the center of the aromatic ring. Theoretical calculations at the MP2/aug-cc-pVTZ level corroborate the experimental results. The origin of attractive interactions was explored by using aromatic rings with a wide range of substituents. The interactions between an oxygen lone pair and an aromatic ring are attractive at van der Waals' distance even with electron-donating substituents. Electron-withdrawing groups increase the strength of the attractive interactions. The results from this study can be only partly rationalized by using the current models of aromatic system. Electrostatic-based models are consistent with the fact that stronger electron-withdrawing groups lead to stronger attractions, but fail to predict or rationalize the fact that weak attractions even exist between electron-rich arenes and oxygen lone pairs. The conclusion from this study is that aromatic rings cannot be treated as a simple quadrupolar functional group at van der Waals' distance. Dispersion forces and local dipole should also be considered.     

Positive ion pair cooperativity exhibited for the binding of phosphate under physiological conditions

The synthesis of a heteroditopic receptor which exhibits positive cooperativity for the binding of phosphate ion pairs under physiological conditions. Optimised complementarity between crown ether host and metal guest leads to increased binding affinity, Ka.     

Channel structure in the new BiCoPO5. Comparison with BiNiPO5. Crystal structure,lone pair localisation and infrared characterisation

The new compound BiCoPO₅, monoclinic, P2₁/n, a = 7.2470(1) A, b = 11.2851(2) A, c = 5.2260(1) A and β = 107.843(1) °, Z = 4, was synthesised and structurally characterised by powder X- ray diffraction and infrared spectroscopy. It is isostructural with bismuth nickel oxyphosphate BiNiOPO₄. The crystal structure is built from a complex tridimensional assembly of (Co/Ni)₂O₁₀ dimers linked by PO₄ groups. This forms large tunnels running along c which host Bi³⁺ cations. Smaller tunnels running along a and crossing the latter were also evidenced. It is noteworthy that the original BiNiPO₅ lattice is appreciably increased with Co²⁺ cations as the transition metal. This feature is essentially pointed out by the Co-O longer distances. The Bi³⁺ cation is surrounded by a strongly distorted oxygen octahedron. Reducing the BiO bonds to the three shortest, Bi environment can be considered as tetrahedral considering the BiO₃Lp polyhedron, Lp = 6s² lone pair (Lp). The lone pair localisation was performed from electrostatic interactions and revealed Lp - Bi distance of 0.68 A and 0.58 A, for Co²⁺ and Ni²⁺ compounds respectively. The infrared spectra of the two compounds are essentially the same and only show slight shifts of the significant bands.     

Predicting ligand binding affinity using on- and off-rates for the SAMPL6 SAMPLing challenge

Interest in ligand binding kinetics has been growing rapidly, as it is being discovered in more and more systems that ligand residence time is the crucial factor governing drug efficacy. Many enhanced sampling methods have been developed with the goal of predicting ligand binding rates (\(k_{\text {on}}\)) and/or ligand unbinding rates (\(k_{\text {off}}\)) through explicit simulation of ligand binding pathways, and these methods work by very different mechanisms. Although there is not yet a blind challenge for ligand binding kinetics, here we take advantage of experimental measurements and rigorously computed benchmarks to compare estimates of \(K_D\) calculated as the ratio of two rates: \(k_{\text {off}}/k_{\text {on}}\). These rates were determined using a new enhanced sampling method based on the weighted ensemble framework that we call “REVO”: Reweighting of Ensembles by Variance Optimization. This is a further development of the WExplore enhanced sampling method, in which trajectory cloning and merging steps are guided not by the definition of sampling regions, but by maximizing trajectory variance. Here we obtain estimates of \(k_{\text {on}}\) and \(k_{\text {off}}\) that are consistent across multiple simulations, with an average log10-scale standard deviation of 0.28 for on-rates and 0.56 for off-rates, which is well within an order of magnitude and far better than previously observed for previous applications of the WExplore algorithm. Our rank ordering of the three host–guest pairs agrees with the reference calculations, however our predicted \(\Delta G\) values were systematically lower than the reference by an average of 4.2 kcal/mol. Using tree network visualizations of the trajectories in the REVO algorithm, and conformation space networks for each system, we analyze the results of our sampling, and hypothesize sources of discrepancy between our \(K_D\) values and the reference. We also motivate the direct inclusion of \(k_{\text {on}}\) and \(k_{\text {off}}\) challenges in future iterations of SAMPL, to further develop the field of ligand binding kinetics prediction and modeling.     

On the Correlation between Photoelectron and Electronic Spectra. Part. II: Experimental indications about the shape of lone pair orbitals

For a π-molecular system containing two symmetry-equivalent heteroatoms, a qualitative relationship between the difference in the n-ionization potentials (ΔIP) and the difference between the n → π* excitation energies (ΔΔE) is derived, using semi-localized orbitals as a basis. The comparison between ΔIP and ΔΔE yields information about the energies and/or the shapes of the two lone pair MO's in the model system. The results provide further insight into ‘through space’ and ‘through bond’ interaction concept introduced by Hoffmann.     

Structural and spectroscopic impact of tuning the stereochemical activity of the lone pair in lead(II) cyanoaurate coordination polymers via ancillary ligands

The reaction of Pb(ClO4)2 x xH2O, an ancillary ligand L, and two equivalents of Au(CN)2(-) gave a series of crystalline coordination polymers, which were structurally characterized. The ligands were chosen to represent a range of increasing basicity, to influence the stereochemical activity (i.e., p-orbital character) of the Pb(II) lone pair. The Pb(II) center in [Pb(1,10-phenanthroline)2][Au(CN)2]2 (1) is 8-coordinate, with a stereochemically inactive lone pair; all 8 Pb-N bonds are similar. The Au(CN)2(-) units propagate a 2-D brick-wall structure. In [Pb(2,2'-bipyridine)2][Au(CN)2]2 (2), the 8-coordinate Pb(II) center has asymmetric Pb-N bond lengths, indicating moderate lone pair stereochemical activity; the supramolecular structure forms a 1-D chain/ribbon motif. For [Pb(ethylenediamine)][Au(CN)2]2 (3), the Pb(II) is only 5-coordinate and extremely asymmetric, with Pb-N bond lengths from 2.123(7) to 3.035(9) A; a rare Pb-Au contact of 3.5494(5) A is also observed. The Au(CN)2(-) units connect the Pb(ethylenediamine) centers to form 1-D zigzag chains which stack via Au-Au interactions of 3.3221(5) A to yield a 2-D sheet. (207)Pb MAS NMR of the polymers indicates an increase in both the chemical shielding span and isotropic chemical shift with increasing Pb(II) coordination sphere anisotropy (from delta iso = -2970 and Omega = 740 for 1 to delta iso = -448 and Omega = 3980 for 3). The shielding anisotropy is positively correlated with Pb(II) p-character, and reflects a direct connection between the NMR parameters and lone-pair activity. Solid-state variable-temperature luminescence measurements indicate that the emission bands at 520 and 494 nm, for 1 and 2, respectively, can be attributed to Pb --> L transitions, by comparison with simple [Pb(L)2](ClO4)2 salts. In contrast, two emission bands for 3 at 408 and 440 nm are assignable to Au-Au and Pb-Au-based transitions, respectively, as supported by single-point density-functional theory calculations on models of 3.