Novel 2-mercaptobenzothiazole and 2-mercaptobenzimidazole-derived Ag16 and Ag18 nanoclusters: synthesis and optical properties.

Silver and gold nanoclusters are promising nanomaterials for various applications such as sensing, catalysis, and bioimaging. However, their synthetic control and repeatability, and determination of their structures are highly complicated. Only a handful of crystal structures of silver nanoclusters (AgNCs) have been reported, while structures of a few others have been reported with the help of mass spectrometry. We synthesized two AgNCs, viz., Ag-MBTNC (Ag16 cluster) and Ag-MBINC (Ag18 cluster) respectively stabilized by 2-mercaptobenzothiazole (2-MBT) and 2-mercaptobenzimidazole (2-MBI) with excellent repeatability; determined their composition and plausible structures using XPS, TGA and MALDI-TOF mass spectrometry; and compared their optical properties. Interestingly, Ag-MBTNC is fluorescent while Ag-MBINC is not, although these are synthesized using stabilizing ligands that have difference in only one atom. The structural features of the clusters are found to be similar but they have contrasting optical behaviours due to the effect of one S atom (in 2-MBT) in place of one N atom (in 2-MBI).

Spodium bonding with noble gas atoms.

The nature of the bonding between a neutral group 12 member (Zn3, Cd3 and Hg3) ring and a noble gas atom was explored using quantum chemical simulations. Natural bond orbital, quantum theory of atoms in molecules, symmetry-adapted perturbation theory, and molecular electrostatic potential surface analysis were also used to investigate the type of interaction between the noble gas atom and the metal rings (Zn3, Cd3 and Hg3). The Zn3, Cd3 and Hg3 rings are bonded to the noble gas through non-covalent interactions, which was revealed by the non-covalent interaction index. Additionally, energy decomposition analysis reveals that dispersion energy is the key factor in stabilizing these systems.

Noble gas dative bonding with coinage metal carbene complexes: A theoretical study.

The structure and stability of noble gas (Ng) bound [NHCM]+ complexes (M = Cu, Ag, and Au) were investigated using Quantum chemical calculations. Dissociation energies, enthalpy, and free energy changes were computed to comprehend the stability of these Ng-bonded complexes. The nature of interactions associated to the bonding between metal and noble gas atoms was studied through the computation of electron density-based descriptors. Detailed electronic structure study revealed electron donation from the noble gas atoms towards the metal center, resulting in the formation of dative bonds.

Coordination of noble gases by alkali-metal-like superatom cation Be3 B.

Quantum chemical calculations were carried out to investigate the noble gas binding ability of Be3 B+ cluster. Calculations reveal that heavier noble gas atoms (ArXe) form stable complexes with this cluster. Detailed bonding analyses reveal that the noble gas atoms act as donor fragment in the formation of Ng → Be donor-acceptor bonds. Three noble gas atoms can consecutively form bonds with the Be atom of the Be3 B+ cluster.

Subtle Chemical Changes Cross the Boundary between Agonist and Antagonist: New A3 Adenosine Receptor Homology Models and Structural Network Analysis Can Predict This Boundary.

Distinguishing compounds' agonistic or antagonistic behavior would be of great utility for the rational discovery of selective modulators. We synthesized truncated nucleoside derivatives and discovered 6c (Ki = 2.40 nM) as a potent human A3 adenosine receptor (hA3AR) agonist, and subtle chemical modification induced a shift from antagonist to agonist. We elucidated this shift by developing new hA3AR homology models that consider the pharmacological profiles of the ligands. Taken together with molecular dynamics (MD) simulation and three-dimensional (3D) structural network analysis of the receptor-ligand complex, the results indicated that the hydrogen bonding with Thr943.36 and His2727.43 could make a stable interaction between the 3'-amino group with TM3 and TM7, and the corresponding induced-fit effects may play important roles in rendering the agonistic effect. Our results provide a more precise understanding of the compounds' actions at the atomic level and a rationale for the design of new drugs with specific pharmacological profiles.

Unsupported Donor-Acceptor Complexes of Noble Gases with Group 13 Elements.

Unsupported donor-acceptor complexes of noble gases (Ng) with group 13 elements have been theoretically studied using density functional theory. Calculations reveal that heavier noble gases form thermodynamically stable compounds. The present study reveals that no rigid framework is necessary to stabilize the donor-acceptor complexes. Rather, prepyramidalization at the Lewis acid center may be an interesting alternative to stabilize these complexes. Detailed bonding analyses reveal the formation of two-center-two-electron dative bonding, where Ng atoms act as a donor.

Ultra-Weak Metal-Metal Bonding: Is There a Beryllium-Beryllium Triple Bond?

Metal-metal triple bonds featuring s-block element have not been reported until now. Only Be-Be double bonds between have been predicted theoretically based on the intuitive electron donation from four s1 type electron-donating ligands. Herein, we theoretically predicted a novel species featuring a Be-Be triple bond in the Li6 Be2 molecule. The molecule was found to be thermodynamically stable. The presence of the triple bond was confirmed by adaptive natural density partitioning (AdNDP), electron localization function (ELF), and atoms in molecules (AIM) analyses. Moreover, the mechanical strength of the Be-Be triple bond was analyzed by using compliance matrix, pointing towards its ultra-weak nature.

Transient receptor potential vanilloid type 1 antagonists: a patent review (2011 - 2014).

INTRODUCTION: Transient receptor potential vanilloid type 1 (TRPV1) is a nonselective cation channel that can be activated by noxious heat, low pH and vanilloid compounds such as capsaicin. Since TRPV1 acts as an integrator of painful stimuli, TRPV1 antagonists can be used as promising therapeutics for new types of analgesics. AREAS COVERED: This review article covers the patents that claim TRPV1 antagonists and were published during 2011 - 2014. The patent evaluation is organized according to the applicant companies, and the representative chemical entities with important in vitro and in vivo data are summarized. EXPERT OPINION: Many pharmaceutical companies showed promising results in the discovery of potent small molecule TRPV1 antagonists, and recently, a number of small molecule TRPV1 antagonists have been advanced into clinical trials. Unfortunately, several candidate molecules showed critical side effects such as hyperthermia and impaired noxious heat sensation in humans, leading to their withdrawal from clinical trials. Some TRPV1 antagonists patented in recent years (2011 - 2014) overcame these undesirable side effects, making the development of TRPV1 antagonists much more promising.

Why nature really chose phosphate.

Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and maintaining the integrity of the genetic material. On the surface, it would appear to be a simple nucleophile displacement reaction. However, this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalyzed reactions. To further complicate matters, while powerful, traditional experimental techniques such as the use of linear free-energy relationships (LFER) or measuring isotope effects cannot make unique distinctions between different potential mechanisms. A quarter of a century has passed since Westheimer wrote his seminal review, 'Why Nature Chose Phosphate' (Science 235 (1987), 1173), and a lot has changed in the field since then. The present review revisits this biologically crucial issue, exploring both relevant enzymatic systems as well as the corresponding chemistry in aqueous solution, and demonstrating that the only way key questions in this field are likely to be resolved is through careful theoretical studies (which of course should be able to reproduce all relevant experimental data). Finally, we demonstrate that the reason that nature really chose phosphate is due to interplay between two counteracting effects: on the one hand, phosphates are negatively charged and the resulting charge-charge repulsion with the attacking nucleophile contributes to the very high barrier for hydrolysis, making phosphate esters among the most inert compounds known. However, biology is not only about reducing the barrier to unfavorable chemical reactions. That is, the same charge-charge repulsion that makes phosphate ester hydrolysis so unfavorable also makes it possible to regulate, by exploiting the electrostatics. This means that phosphate ester hydrolysis can not only be turned on, but also be turned off, by fine tuning the electrostatic environment and the present review demonstrates numerous examples where this is the case. Without this capacity for regulation, it would be impossible to have for instance a signaling or metabolic cascade, where the action of each participant is determined by the fine-tuned activity of the previous piece in the production line. This makes phosphate esters the ideal compounds to facilitate life as we know it.

Ketosteroid isomerase provides further support for the idea that enzymes work by electrostatic preorganization.

One of the best systems for exploring the origin of enzyme catalysis has been the reaction of ketosteroid isomerase (KSI). Studies of the binding of phenolates to KSI have been taken as proof that the electrostatic preorganization effect only makes a minor contribution to the binding of the real, multiring, transition state (TS). However, our simulation study has determined that the difference between the phenolates and the TS arises from the fact that the nonpolar state of the phenolate can rotate freely relative to the oxyanion hole and thus loses the preorganization contribution. A recent study explored the reactivity of both small and multiring systems and concluded that their similar reactivity contradicts our preorganization idea. Herein, we establish that the available experiments in fact provide what is perhaps the best proof and clarification of the preorganization idea and its crucial role in enzyme catalysis. First, we analyze the binding energy and the pK(a) of equilenin and identify direct experimental evidence for our prediction about the differential electrostatic stabilization of the large TS and the small phenolates. Subsequently, we show that the similar reactivity of the small and large systems is also due to an electrostatic preorganization effect but that this effect only appears in the intermediate state because the TS is not free to rotate. This establishes the electrostatic origin of enzyme catalysis. We also clarify the crucial importance of having a well-defined physical concept when examining catalytic effects and the need for quantitative tools for analyzing such effects.

Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase.

Gaining detailed understanding of the energetics of the proton-pumping process in cytochrome c oxidase (CcO) is one of the challenges of modern biophysics. Despite promising mechanistic proposals, most works have not related the activation barriers of the different assumed steps to the protein structure, and there has not been a physically consistent model that reproduced the barriers needed to create a working pump. This work reevaluates the activation barriers for the primary proton transfer (PT) steps by calculations that reflect all relevant free energy contributions, including the electrostatic energies of the generated charges, the energies of water insertion, and large structural rearrangements of the donor and acceptor. The calculations have reproduced barriers that account for the directionality and sequence of events in the primary PT in CcO. It has also been found that the PT from Glu-286 (E) to the propionate of heme a(3) (Prd) provides a gate for an initial back leakage from the high pH side of the membrane. Interestingly, the rotation of E that brings it closer to Prd appears to provide a way for blocking competing pathways in the primary PT. Our study elucidates and quantifies the nature of the control of the directionality in the primary PT in CcO and provides instructive insight into the role of the water molecules in biological PT, showing that "bridges" of several water molecules in hydrophobic regions present a problem (rather than a solution) that is minimized in the primary PT.

The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all.

The light-induced proton transport in bacteriorhodopsin has been considered as a model for other light-induced proton pumps. However, the exact nature of this process is still unclear. For example, it is not entirely clear what the driving force of the initial proton transfer is and, in particular, whether it reflects electrostatic forces or other effects. The present work simulates the primary proton transfer (PT) by a specialized combination of the EVB and the QCFF/PI methods. This combination allows us to obtain sufficient sampling and a quantitative free energy profile for the PT at different protein configurations. The calculated profiles provide new insight about energetics of the primary PT and its coupling to the protein conformational changes. Our finding confirms the tentative analysis of an earlier work (A. Warshel, Conversion of light energy to electrostatic energy in the proton pump of Halobacterium halobium, Photochem. Photobiol. 30 (1979) 285-290) and determines that the overall PT process is driven by the energetics of the charge separation between the Schiff base and its counterion Asp85. Apparently, the light-induced relaxation of the steric energy of the chromophore leads to an increase in the ion-pair distance, and this drives the PT process. Our use of the linear response approximation allows us to estimate the change in the protein conformational energy and provides the first computational description of the coupling between the protein structural changes and the PT process. It is also found that the PT is not driven by twist-modulated changes of the Schiff base's pKa, changes in the hydrogen bond directionality, or other non-electrostatic effects. Overall, based on a consistent use of structural information as the starting point for converging free energy calculations, we conclude that the primary event should be described as a light-induced formation of an unstable ground state, whose relaxation leads to charge separation and to the destabilization of the ion-pair state. This provides the driving force for the subsequent PT steps.

A new paradigm for electrostatic catalysis of radical reactions in vitamin B12 enzymes.

The catalytic power of enzymes containing coenzyme B(12) cofactor has been, in some respects, the "last bastion" for the strain hypothesis. The present work explores the origin of this effect by using simulation methods that overcome the sampling difficulties of previous energy minimization studies. It is found that the major part of the catalytic effect is due to the electrostatic interaction between the ribose and the protein, and that the strain contribution is very small. Remarkably, enzymes can use electrostatic effects even in a radical process, when the charge distribution of the reacting fragments does not change significantly during the reaction. Electrostatic catalysis can, in such cases, be obtained by attaching a polar group to the leaving fragment and designing an active site that interacts more strongly with this group in the product state than in the reactant state. The finding that evolution had to use this trick provides further evidence to the observation that it is extremely hard to catalyze enzymatic reactions by nonelectrostatic factors. The trick used by B(12) enzymes may, in fact, be a very powerful new strategy in enzyme design.

Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomerase.

The relationship between binding of transition state analogues (TSAs) and catalysis is an open problem. A recent study of the binding of phenolate TSAs to ketosteroid isomerase (KSI) found a small change in the binding energy with a change in charge delocalization of the TSAs. This has been taken as proof that electrostatic effects do not contribute in a major way to catalysis. Here we reanalyze the relationship between the binding of the TSAs and the chemical catalysis by KSI as well as the binding of the transition state (TS), by computer simulation approaches. Since the simulations reproduce the relevant experimental results, they can be used to quantify the different contributions to the observed effects. It is found that the binding of the TSA and the chemical catalysis represent different thermodynamic cycles with very different electrostatic contributions. While the binding of the TSA involves a small electrostatic contribution, the chemical catalysis involves a charge transfer process and a major electrostatic contribution due to the preorganization of the active site. Furthermore, it is found that the electrostatic preorganization contributions to the binding of the enolate intermediate of KSI and the TS are much larger than the corresponding effect for the binding of the TSAs. This reflects the dependence of the preorganization on the orientation of the nonpolar form of the TSAs relative to the oxyanion hole. It seems to us that this work provides an excellent example of the need for computational studies in analyzing key experimental findings about enzyme catalysis.

Modeling electrostatic effects in proteins.

Electrostatic energies provide what is perhaps the most effective tool for structure-function correlation of biological molecules. This review considers the current state of simulations of electrostatic energies in macromolecules as well as the early developments of this field. We focus on the relationship between microscopic and macroscopic models, considering the convergence problems of the microscopic models and the fact that the dielectric 'constants' in semimacroscopic models depend on the definition and the specific treatment. The advances and the challenges in the field are illustrated considering a wide range of functional properties including pK(a)'s, redox potentials, ion and proton channels, enzyme catalysis, ligand binding and protein stability. We conclude by pointing out that, despite the current problems and the significant misunderstandings in the field, there is an overall progress that should lead eventually to quantitative descriptions of electrostatic effects in proteins and thus to quantitative descriptions of the function of proteins.

Ferromagnetic bonding: high spin copper clusters (n+1)Cu(n); n = 2-14) devoid of electron pairs but possessing strong bonding.

Density functional theoretic studies are performed for the high-spin copper clusters (n)(+1)Cu(n) (n = 2-14), which are devoid of electron pairs shared between atoms, hence no-pair clusters (J. Phys. Chem. 1988, 92, 1352; Isr. J. Chem. 1993, 33, 455; J. Am. Chem. Soc. 1999, 121, 3165). Despite the lack of electron pairing, it is found that the bond dissociation energy per atom (BDE/n) is significant and converges (to within 1 kcal mol(-1)), around a cluster size (11)Cu(10), to a value of BDE/n = 19 kcal mol(-1). This is a very large bonding energy, much larger than has previously been obtained for no-pair clusters of lithium, BDE/n = 12 kcal mol(-1), or sodium clusters, BDE/n = 3 kcal mol(-1). This bonding, so-called ferromagnetic bonding (FM-bonding) is analyzed using a valence bond (VB) model (J. Phys. Chem. A 2002, 106, 4961; Phys. Chem. Chem. Phys. 2003, 5, 158). As such, FM-bonding in no-pair clusters is described as an ionic fluctuation, of the triplet pair, that spreads over all the close neighbors of a given atom in the clusters. Thus, if we refer to each triplet pair and its ionic fluctuations as a local FM-bond, we can regard the electronic structure of a given (n)(+1)M(n) cluster as a resonance hybrid of all the local FM-bonds between close neighbors. The model shows how a weak interaction in the diatomic triplet molecule can become a remarkably strong binding force that binds together mono-valent atoms without even a single electron pair. This is achieved because the growing number of VB structures exerts a cumulative effect of stabilization that is maximized when the cluster has a compact structure with an optimal coordination number for the atoms.

What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome?

The action of the peptidyl transferase center of the large ribosomal unit presents a fundamental step in the evolution from the RNA world to the protein world. Thus, it is important to understand the origin of the catalytic power of this ancient enzyme. Earlier studies suggested that the ribosome catalyzes peptide bond formation by using one of its groups as a general base, while more recent works have proposed that the catalysis is due to proximity effects or to substrate-assisted catalysis. However, the actual nature of the catalytic mechanism remains controversial. This work addresses the origin of the catalytic power of the ribosome by using computer simulation approaches and comparing the energetics of the peptide bond formation in the ribosome and in water. It is found that a significant part of the observed activation entropy of the reference solution reaction is due to solvation entropy, and that the proximity effect is smaller than previously thought. It is also found that the 2'-OH of the A76 ribose, which is associated with a large rate acceleration in the ribosome reaction, does not catalyze peptide bond formation in water. Thus, the catalytic effect cannot be attributed to substrate-assisted catalysis but rather to the effect of the ribosome on the reacting system. Overall, our calculations indicate that the reduction of the activation free energy is mainly due to electrostatic effects. The nature of these effects and their relationship to catalytic factors in modern enzymes is analyzed and discussed.

Sulfoxidation mechanisms catalyzed by cytochrome P450 and horseradish peroxidase models: spin selection induced by the ligand.

The sulfoxidation of dimethyl sulfide (DMS), by two different heme-type enzyme models (without the protein), namely, horseradish peroxidase (HRP) and cytochrome P450 (P450), was studied using density functional theory. The models differ from each other by the axial ligand of the iron, which is imidazole in the case of HRP and thiolate in the case of P450. The computational results reveal a concerted oxygen atom transfer to sulfur, with spin-state selection dependent upon the identity of the proximal ligand. In the case of thiolate, the mechanism prefers the high-spin quartet pathway; whereas in the case of imidazole, the mechanism involves two-state reactivity (TSR), with competing quartet and doublet spin states. Furthermore, with thiolate the high-spin transition state, (4)TS(P450), has an upright conformation with a large Fe-O-S(DMS) angle of 147 degrees , whereas the low-spin species, (2)TS(P450), has a small angle and its Fe-O moiety makes an O-N(Por) bond with one of the nitrogen atoms of the porphine macrocycle. By contrast, when the proximal ligand is imidazole, both transition states possess a bent Fe-O bond and an O-N(Por) bond. These spin-state selection patterns obey simple orbital-selection rules, which are manifestations of the electronic nature of the ligand, i.e., the electron-releasing effect of the thiolate vis-a-vis the electron-withdrawal effect of imidazole. Other possible reactivity expressions of the spin-selection patterns are discussed [Dowers, T. S., Rock, D. A., Rock, D. A., Jones, J. P. (2004) J. Am. Chem. Soc. 126, 8868-8869]. Theory shows that intrinsically, HRP should be as reactive as P450 toward sulfoxidation.

Simulating redox coupled proton transfer in cytochrome c oxidase: looking for the proton bottleneck.

Gaining a detailed understanding of the molecular nature of the redox coupled proton transfer in cytochrome c oxidase (COX) is one of the challenges of modern biophysics. The present work addresses this by integrating approaches for simulations of proton transport (PTR) and electron transfer (ET). The resulting method converts the electrostatic energies of different charge configurations and reorganization energies to free-energy profiles for different PTR and ET pathways. This approach provides for the first time a tool to study the actual activation barriers and kinetics of different feasible PTR processes in the cycle of COX. Using this tool, we explore the PTR through the bottleneck water molecules. It is found that a stepwise PTR along this commonly assumed path leads to far too high barriers and is, thus, inconsistent with the observed kinetics. Furthermore, the simulated free-energy profile does not provide a simple gating mechanism. Fortunately, we obtain reasonable kinetics when we consider a PTR that involves a concerted transfer of protons to and from E286. Finally, semi-qualitative considerations of the forward and backward barriers point toward open questions about the actual gating process and offer a feasible pumping mechanism. Although further studies are clearly needed, we believe that our approach offers a general and effective tool for correlating the structure of COX with its function.