New Methodology to Produce Sets of Valence Bond Structures with Enhanced Chemical Insights.

The valence bond (VB) theory uses localized orbitals, and its wave function is composed of a linear combination of various VB structures which are based on sets of spin functions. The VB structures are not unique, and different sets are used, Rumer sets being the most common for classical VB due to their advantage as being both easily obtained as linearly independent and meaningful. Yet, Rumer rules, which are responsible for the simplified process of obtaining the Rumer sets, are very restrictive. Furthermore, Rumer sets are best suited for cyclic systems; however, in noncyclic systems, structures resulting from Rumer rules are often not the most intuitive/suitable structures for these systems. We have developed a method to obtain chemically insightful structures, which is based on concepts of chemical bonding. The method provides sets of VB structures with improved chemical insight, which can also be controlled. Parallel to the Rumer structures, the chemical insight sets of structures are based on electron pair coupling, and hence, pictorially can be drawn similarly to the Lewis structures. Yet, different from Rumer rules, the chemical insight method, being more flexible, allows larger combinations of bonds as well as larger combinations of structures in the sets it offers, resulting in many more possible sets that are better adapted to the systems studied.

The effect of immediate environment on bond strength of different bond types-A valence bond study.

The ability to design catalysis largely depends on our understanding of the electrostatic effect of the surrounding on the bonds participating in the reaction. Here, we used a simplistic model of point charges (PCs) to determine a set of rules guiding how to construct PC-bond arrangement that can strengthen or weaken different chemical bonds. Using valence bond theory to calculate the in situ bond energies, we show that the effect of the PC mainly depends on the bond's dipole moment irrespective of its type (being covalent or charge shift). That is, polar bonds are getting stronger or weaker depending on the sign and location of the PC, whereas non- or weakly polar bonds become stronger or weaker depending only on the location of the PC and to a smaller extent compared with polar bonds. We also show that for polar bonds, the maximal bond strengthening and weakening effect can be achieved when the PC is placed along the bond axis, as close as possible to the more and less polarizable atom/fragment, respectively. Finally, due to the stabilizing effects of polarizability, we show that, overall, it is easier to cause bond strengthening compared with bond weakening. Particularly, for polar bonds, bond strengthening is larger than bond weakening obtained by an oppositely signed PC. These rules should be useful in the future design of catalysis in, e.g., enzyme active sites.

Hydrolytically Stable and Cytotoxic [ONON]2Ti(IV)-Type Octahedral Complexes.

A new family of titanium(IV) complexes based on [ONON] diaminobis(phenolato) ligands with Me, Br, Cl, and F ortho substitutions was synthesized and characterized. X-ray structures of three derivatives revealed homoleptic L2Ti-type compounds that exhibit an octahedral geometry without binding of the dangling amine unit. DFT calculations demonstrated that the preference of an L2Ti complex is not driven by solvent or ligand substitutions but rather by entropic effects. Except for the fluorinated derivative that was hydrolyzed immediately following water addition at room temperature and had the lowest biological activity of the series tested, all other complexes showed cytotoxic activity comparable to or higher than (up to 10-fold) that of cisplatin toward human ovarian A2780 and colon HT-29 cancer cell lines (IC50 values: 0.6-13 µM after incubation for 72 h). Activity was generally higher (up to 10-fold) toward the more sensitive ovarian line and similar for all active complexes, whereas differences were recorded toward the colon line that are attributed to bioavailability variations among the complexes analyzed. Particularly high hydrolytic stability was recorded for the brominated derivative with a t1/2 of 17 ± 1 days for ligand hydrolysis in 10% D2O at room temperature, relative to t1/2 of 56 ± 5 and 22 ± 6 h measured for the chlorinated and methylated derivatives, respectively. Altogether this series of compounds represent a promising family of anticancer agents, with the chlorinated derivative showing the best combination of stability, cytotoxicity, and bioavailability.

Osteogenic growth peptide is a potent anti-inflammatory and bone preserving hormone via cannabinoid receptor type 2.

The endocannabinoid system consists mainly of 2-arachidonoylglycerol and anandamide, as well as cannabinoid receptor type 1 and type 2 (CB2). Based on previous studies, we hypothesized that a circulating peptide previously identified as osteogenic growth peptide (OGP) maintains a bone-protective CB2 tone. We tested OGP activity in mouse models and cells, and in human osteoblasts. We show that the OGP effects on osteoblast proliferation, osteoclastogenesis, and macrophage inflammation in vitro, as well as rescue of ovariectomy-induced bone loss and prevention of ear edema in vivo are all abrogated by genetic or pharmacological ablation of CB2. We also demonstrate that OGP binds at CB2 and may act as both an agonist and positive allosteric modulator in the presence of other lipophilic agonists. In premenopausal women, OGP circulating levels significantly decline with age. In adult mice, exogenous administration of OGP completely prevented age-related bone loss. Our findings suggest that OGP attenuates age-related bone loss by maintaining a skeletal CB2 tone. Importantly, they also indicate the occurrence of an endogenous peptide that signals via CB2 receptor in health and disease.

HU-446 and HU-465, Derivatives of the Non-psychoactive Cannabinoid Cannabidiol, Decrease the Activation of Encephalitogenic T Cells.

Cannabidiol (CBD), the non-psychoactive cannabinoid, has been previously shown by us to decrease peripheral inflammation and neuroinflammation in mouse experimental autoimmune encephalomyelitis (EAE) model of multiple sclerosis (MS). Here we have studied the anti-inflammatory effects of newly synthesized derivatives of natural (-)-CBD ((-)-8,9-dihydro-7-hydroxy-CBD; HU-446) and of synthetic (+)-CBD ((+)-8,9-dihydro-7-hydroxy-CBD; HU-465) on activated myelin oligodendrocyte glycoprotein (MOG)35-55-specific mouse encephalitogenic T cells (T(MOG) ) driving EAE/MS-like pathologies. Binding assays followed by molecular modeling revealed that HU-446 has negligible affinity toward the cannabinoid CB1 and CB2 receptors while HU-465 binds to both CB1 and CB2 receptors at the high nanomolar concentrations (Ki = 76.7 ± 5.8 nm and 12.1 ± 2.3 nm, respectively). Both, HU-446 and HU-465, at 5 and 10 µm (but not at 0.1 and 1 µm), inhibited the MOG35-55-induced proliferation of autoreactive T(MOG) cells via CB1/CB2 receptor independent mechanisms. Moreover, both HU-446 and HU-465, at 5 and 10 µm, inhibited the release of IL-17, a key autoimmune cytokine, from MOG35-55-stimulated T(MOG) cells. These results suggest that HU-446 and HU-465 have anti-inflammatory potential in inflammatory and autoimmune diseases.

Challenges within the linear response approximation when studying enzyme catalysis and effects of mutations.

Various aspects of the linear response approximation (LRA) approach were examined when calculating reaction barriers within an enzyme and its different mutants. Scaling the electrostatic interactions is shown to slightly affect the absolute values of the barriers but not the overall trend when comparing wild-type and mutants. Convergence of the overall energetics was shown to depend on the sampling. Finally, the contribution of particular residues was shown to be significant, despite its small value.

CB2 cannabinoid receptor agonist enantiomers HU-433 and HU-308: An inverse relationship between binding affinity and biological potency.

Activation of the CB2 receptor is apparently an endogenous protective mechanism. Thus, it restrains inflammation and protects the skeleton against age-related bone loss. However, the endogenous cannabinoids, as well as Δ(9)-tetrahydrocannabinol, the main plant psychoactive constituent, activate both cannabinoid receptors, CB1 and CB2. HU-308 was among the first synthetic, selective CB2 agonists. HU-308 is antiosteoporotic and antiinflammatory. Here we show that the HU-308 enantiomer, designated HU-433, is 3-4 orders of magnitude more potent in osteoblast proliferation and osteoclast differentiation culture systems, as well as in mouse models, for the rescue of ovariectomy-induced bone loss and ear inflammation. HU-433 retains the HU-308 specificity for CB2, as shown by its failure to bind to the CB1 cannabinoid receptor, and has no activity in CB2-deficient cells and animals. Surprisingly, the CB2 binding affinity of HU-433 in terms of [(3)H]CP55,940 displacement and its effect on [(35)S]GTPγS accumulation is substantially lower compared with HU-308. A molecular-modeling analysis suggests that HU-433 and -308 have two different binding conformations within CB2, with one of them possibly responsible for the affinity difference, involving [(35)S]GTPγS and cAMP synthesis. Hence, different ligands may have different orientations relative to the same binding site. This situation questions the usefulness of universal radioligands for comparative binding studies. Moreover, orientation-targeted ligands have promising potential for the pharmacological activation of distinct processes.

Valence bond and enzyme catalysis: a time to break down and a time to build up.

Understanding enzyme catalysis and developing ability to control of it are two great challenges in biochemistry. A few successful examples of computational-based enzyme design have proved the fantastic potential of computational approaches in this field, however, relatively modest rate enhancements have been reported and the further development of complementary methods is still required. Herein we propose a conceptually simple scheme to identify the specific role that each residue plays in catalysis. The scheme is based on a breakdown of the total catalytic effect into contributions of individual protein residues, which are further decomposed into chemically interpretable components by using valence bond theory. The scheme is shown to shed light on the origin of catalysis in wild-type haloalkane dehalogenase (wt-DhlA) and its mutants. Furthermore, the understanding gained through our scheme is shown to have great potential in facilitating the selection of non-optimal sites for catalysis and suggesting effective mutations to enhance the enzymatic rate.

How valence bond theory can help you understand your (bio)chemical reaction.

Almost a century has passed since valence bond (VB) theory was originally introduced to explain covalent bonding in the H2 molecule within a quantum mechanical framework. The past century has seen constant improvements in this theory, with no less than two distinct Nobel prizes based on work that is essentially developments in VB theory. Additionally, ongoing advances in both methodology and computational power have greatly expanded the scope of problems that VB theory can address. In this Tutorial Review, we aim to give the reader a solid understanding of the foundations of modern VB theory, using a didactic example of a model SN2 reaction to illustrate its immediate applications. This will be complemented by examples of challenging problems that at present can only be efficiently addressed by VB-based approaches. Finally, the ongoing importance of VB theory is demonstrated. It is concluded that VB will continue to be a major driving force for chemistry in the century to come.

Aqueous stability of alumina and silica perhydrate hydrogels: experiments and computations.

Alumina and silica perhydrate hydrogels were synthesized. Raman spectroscopy and solid (27)Al MAS NMR confirmed alumina perhydrate formation. Thermal and aqueous stability of alumina and silica perhydrates was studied, and they showed exceptionally high stabilities. Alumina perhydrate retained some of the hydrogen peroxide even at 170 °C, higher than any other reported perhydrate, whereas the silica perhydrate lost its hydrogen peroxide content already at 90 °C. The silica perhydrate lost all its peroxide content upon immersion in water, whereas the alumina perhydrate was stable under near-neutral pH conditions. A computational study was conducted in order to glean molecular insight into the observed thermal and aqueous stability of alumina compared to silica perhydrate. Comparison of the hydrogen bond features and the stabilization energies of the hydrate and perhydrate of silica and alumina revealed a higher preference for hydrogen peroxide over water by alumina relative to silica. This is shown to be due to hydrogen peroxide being a better hydrogen donor than water and due to the superior hydrogen accepting propensity of alumina compared to silica.

Copper-chaperones with dicoordinated Cu(I)--unique protection mechanism.

Cu(I) dicoordination with thiolate ligands is not common. Yet, different from its homologue proteins, human copper chaperone is known to bind Cu(I) using this low coordination number while binding Cu(I) only via the two conserved Cysteine residues, Cys12 and Cys15. Based on structural analysis, this work determines that the protein possesses two distinct conformations referred to as "in" and "out" due to the relative positioning of Cys12 (one of Cu(I) binding residues). The "out" conformation, with Cys12 pointing out, imposes a buried Cu(I) position, whereas the "in" conformation with Cys12 pointing inwards results in a more exposed Cu(I) thus, available for transfer. Using QM/MM methods along with thermodynamic cycles these two conformations are shown to exhibit different coordination preference, suggesting that the protein has evolved to have a unique Cu(I) protection mechanism. It is proposed that the "out" conformation with a preference to dicoordination prevents Cu(I) interaction with external ligands and/or Cu(I) release to the solvent, whereas the "in" conformation with preference to tricoordinated Cu(I), facilitates Cu(I) transfer to target proteins, where additional ligands are involved.

Predicting the coordination number within copper chaperones: Atox1 as case study.

The concentration of copper ions in biological systems is tightly regulated by metallochaperone proteins which are responsible for Cu(I) delivery to designated locations in the cell. These proteins contain a unique motif (MXCXXC) that binds Cu(I) very tightly and specifically but at the same time allows efficient metal transfer to target proteins that often contain a similar copper binding motif. It was found that binding to Cu(I) is achieved through the two cysteine residues in a low coordination number of 2-3 due to possible binding of a third external ligand. Understanding copper transport requires better understanding of copper coordination. Here we therefore focused on establishing a computational method that can predict the coordination number of copper in copper chaperones. The method is shown to be successful in predicting the coordination of Cu(I) within the human copper chaperone (Atox1). Based on the results, a possible rationale for this unique Cu(I) dicoordination in Atox1 is suggested.

Calculation of transition dipole moment in fluorescent proteins--towards efficient energy transfer.

Förster Resonance Energy Transfer (FRET) between fluorescent proteins (FPs) is widely used to construct fluorescent sensor proteins, to study intracellular protein-protein interactions and to monitor conformational changes in multidomain proteins. Although FRET depends strongly on the orientation of the transition dipole moments (TDMs) of the donor and acceptor fluorophores, this orientation dependence is currently not taken into account in FRET sensor design. Similarly, studies that use FRET to derive structural constrains typically assume a κ(2) of 2/3 or use the TDM of green fluorescent protein, as this is the only FP for which the TDM has been determined experimentally. Here we used time-dependent density functional theory (TD-DFT) methods to calculate the TDM for a comprehensive list of commonly used fluorescent proteins. The method was validated against higher levels of calculation. Validation with model compounds and the experimentally determined TDM of GFP shows that the TDM is mostly determined by the structure of the π-conjugated fluorophore and is insensitive to non-conjugated side chains or the protein surrounding. Our calculations not only provide TDM for most of the currently used FPs, but also suggest an empirical rule that can be used to obtain the TDMs for newly developed fluorescent proteins in the future.

Hydrolysis of organophosphate compounds by mutant butyrylcholinesterase: a story of two histidines.

This study is aimed at understanding the hydrolysis mechanism of organophosphate (OP) compounds by G117H-BChE. It is a theoretical study that focuses on the role of the G117H mutation in the dephosphorylation step. Various proposed mechanisms are examined. We show that His117 acts as a general base by activating a water molecule, and thus assisting its nucleophilic attack on the phosphate. The calculated reaction energy profile agrees well with the experimental data. Moreover, analysis of the reaction via its two hypothetical elementary steps, proton transfer and hydroxide attack, supports the role of His117 as a general base. Further support to the proposed mechanism is gained by structural comparison of the active site to RNAse A, which has similar composition of substrate and functional groups. The similarity between these enzymes extends beyond the structure and also becomes evident when comparing functionality of various active sites residues as well as rate-pH dependence obtained in the two cases. Moreover, it is demonstrated that an extended form of Bevilacqua's model (Biochemistry 2003;42:2259-2265) may resolve the apparent contradictions between the proposed mechanism and various experimental observations regarding rate-pH dependence. Finally, that same model is shown to rationalize the hydrolase activity of G117D BChE, an observation which is considered puzzling. It is concluded that G117H-BChE hydrolyzes echothiophate and possibly other OP compounds via a general acid-base mechanism. On the basis of this mechanism, one can now proceed with rational design aimed at improving the enzyme by exploiting both the structural and mechanistic knowledge.

VB/MM protein landscapes: a study of the S(N)2 reaction in haloalkane dehalogenase.

QM/MM methods are widely used for studies of reaction mechanisms in water and protein environments. Recently, we have developed the VB/MM method in which the QM part is implemented by the ab initio valence bond (VB) method. Here, we report on further improvement of the VB/MM method which makes it possible to use the method for reactivity studies in systems where the QM and MM parts are connected by covalent bonds followed by first ab initio VB study of reactivity in proteins. We implemented a simple link atom scheme to treat the boundary interactions. We tested the performance of the link atom treatment in combination with the VB/MM method on an S(N)2 reaction and found it to be sufficiently accurate. We then used the VB/MM method to study the S(N)2 reaction in haloalkane dehalogenase (DhlA). We show that the predicted reaction barrier heights are in good agreement with estimated experimental values, thereby validating the method. Finally, we analyze the reaction energetics in terms of contributions of the VB configurations and conclude that such analysis is instrumental in pinpointing the essential features of the catalytic mechanism.

Can DFT methods correctly and efficiently predict the coordination number of copper(I) complexes? A case study.

The coordination number of various experimentally known Cu(I) compounds is studied using density functional theory. Various basis sets are tested, aiming to establish a reliable level for prediction of the coordination number of these and other Cu(I) complexes. It is found that most levels exhibit correct trends, namely, the bulkier ligands demonstrate larger preference for coordination of two ligands. Proper absolute values are obtained when dispersion corrections are also included in the calculations. It is concluded that the fairly small modified 6-31+G* basis set due to Pulay represents a good compromise between accuracy and efficiency, followed by Balabanov and Peterson's all-electron aug-cc-pVDZ basis set. The overall energy is decomposed into various components whose relative contribution to the overall tendency of forming a complex with a particular coordination is examined. It is shown that two opposing contributions play a major role: the interaction energy of the ligand being added and the deformation energy of the copper's coordination sphere prior to the ligand addition. The former being a stabilizing contribution, leads to higher coordination numbers while the later, a destabilizing contribution, is shown to favor lower coordination numbers.

The structure of G117H mutant of butyrylcholinesterase: nerve agents scavenger.

Organophosphate ester (OP) compounds are known for their ubiquitous use as insecticides. At the same time, these chemicals are highly toxic and can be used as nerve agents. G117H mutant of human Butyrylcholinesterase (BChE) was found to be capable of hydrolyzing certain OPs and protect against their toxicity. However, for therapeutic use, the rate of hydrolysis is too low. Its catalytic power can be improved by rational design, but the structure of the G117H mutant is first required. In this work, we determined, computationally, the three dimensional structure of the G117H BChE mutant. The structure was then validated by simulating acetylation of acetylthiocholine (ATC). Several plausible conformers of G117H BChE were examined but only the (62,-75) conformer fully reproduced catalytic effect. The (62,-75) conformer is, therefore, suggested as the structure adopted by the G117H BChE mutant. This conformer is shown to explain the loss of esterase activity observed for the G122H Acetylcholinesterase mutant together with its recovery when additional mutations are placed turning the enzyme also into an OP hydrolase. Furthermore, similarity of the structure to the structure of RNase A, which is known to hydrolyze the O--P bond in RNA, grants it further credibility and suggests a mechanism for the OP hydrolysis.

VB/MM--the validity of the underlying approximations.

Two recently developed methods, VB/MM and density embedded VB/MM (DE-VB/MM), are compared, and their respective approximations are examined. The two methods combine valence-bond (VB) calculations with molecular mechanics (MM) and aim to allow VB analysis of reactions in large biological environments. Furthermore, the two methods utilize two major approximations regarding both the overlap and the reduced resonance integral between the various VB configurations. The difference between the two methods, however, is that VB/MM employs these approximations for the overall interaction of the reacting fragments with their surrounding, whereas DE-VB/MM employs the approximations only with regards to the van der Waals (VdW) interactions whereas the electrostatic interactions are calculated rigorously at the quantum level. The approximations that lay the grounds for the two methods involve the assumption that the overlap between the VB configurations and the respective reduced resonance integral are both invariant to the environment. Similar approximations are utilized in several other VB-based QM/MM methods. However, although extensively used, these approximations were never rigorously proved. Here, we exploit the development of the DE-VB/MM method to numerically examine the approximations by calculating the accurate as well as the approximated values of overlap and reduced resonance integral for systems where the environment involves only electrostatic interactions. The quality of the approximations is examined together with their effect on the absolute energies, the wave function, and the overall energetics. Three test cases are chosen, the dissociation of CH 3F and LiF and the identity S N2 reaction. It is shown that the approximations are usually good with the exception of cases where extreme changes are expected in the wave function. Furthermore, the impact of the approximations on the overall wave function and the overall energetics is found to be quite small. It is concluded that VB/MM, where the approximations are used more extensively, can serve as the first method of choice.

A VB/MM view of the identity S(N)2 valence-bond state correlation diagram in aqueous solution.

The valence-bond state correlation diagram (VBSCD), which was developed by Shaik and co-workers is an excellent tool to understand reactivity patterns in chemical reactions. The strength of the model is in its ability to describe the whole spectrum of reaction types and unify them under a single general paradigm. Moreover, it allows one to understand, conceptualize, and predict chemical reactivity in a general as well as specific manner. As such, VBSCD is a valuable model. The model has been largely tested on various systems in the gas phase both qualitatively and quantitatively. However, its application to reactions in solution was given less attention because of the difficulties to represent solvent reorganization and estimate non-equilibrium solvation effects, which, on the basis of the model, are expected to be fundamental. The recently developed valence-bond molecular mechanics (VB/MM) method overcomes these difficulties because it involves explicit solvent molecules and thus allows quantitative examination of these solvent effects. This work presents a study of the identity S(N)2 reaction X(-) + H(3)CX --> XCH(3) + X(-); (X = F, Cl, Br, I) in aqueous solution. The various parameters that form the VBSCD model are calculated and compared with the corresponding model's estimated values. A relatively good agreement between the calculated and estimated values is found. It is shown that when facing quantitative considerations, the picture may not be as simplistic as in the qualitative study; yet, the fundamental nature of the description is unaffected. This indicates that combined together, the VB/MM approach and the VBSCD model offer a very powerful tool to study reactions in complex systems and understand their reactivity patterns.

Density embedded VB/MM: a hybrid ab initio VB/MM with electrostatic embedding.

A hybrid QM/MM method that combines ab initio valence-bond (VB) with molecular mechanics (MM) is presented. The method utilizes the ab initio VB approach to describe the reactive fragments and MM to describe the environment thus allows VB calculations of reactions in large biological systems. The method, termed density embedded VB/MM (DE-VB/MM), is an extension of the recently developed VB/MM method. It involves calculation of the electrostatic interaction between the reactive fragments and their environment using the electrostatic embedding scheme. Namely, the electrostatic interactions are represented as one-electron integrals in the ab initio VB Hamiltonian, hence taking into account the wave function polarization of the reactive fragments due to the environment. Moreover, the assumptions that were utilized in an earlier version of the method, VB/MM, to formulate the electrostatic interactions effect on the off-diagonal matrix elements are no longer required in the DE-VB/MM methodology. Using DE-VB/MM, one can calculate, in addition to the adiabatic ground state reaction profile, the energy of the diabatic VB configurations as well as the VB state correlation diagram for the reaction. The abilities of the method are exemplified on the identity SN2 reaction of a chloride anion with methyl chloride in aqueous solution. Both the VB configurations diagram and the state correlation diagram are presented. The results are shown to be in very good agreement with both experimental and other computational data, suggesting that DE-VB/MM is a proper method for application to different reactivity problems in biological systems.