Calibration of the dianionic phosphate group: Validation on the recognition site of the homodimeric enzyme phosphoglucose isomerase

We calibrate and validate the parameters necessary to represent the dianionic phosphate group (DPG) in molecular mechanics. DPG is an essential fragment of signaling biological molecules and protein-binding ligands. It is a constitutive fragment of biosensors, which bind to the dimer interface of phosphoglucose isomerase (PGI), an intracellular enzyme involved in sugar metabolism, as well as an extracellular protein known as autocrine motility factor (AMF) closely related to metastasis formation. Our long-term objective is to design DPG-based biosensors with enhanced affinities for AMF/PGI cancer biomarker in blood. Molecular dynamics with polarizable potentials could be used toward this aim. This requires to first evaluate the accuracy of such potentials upon representing the interactions of DPG with its PGI ligands and tightly bound water molecules. Such evaluations are done by comparisons with high-level ab initio quantum chemistry (QC) calculations. We focus on the Sum of Interactions Between Fragments Ab initio computed (SIBFA) polarizable molecular mechanics procedure. We present first the results of the DPG calibration. This is followed by comparisons between ΔE(SIBFA) and ΔE(QC) regarding bi-molecular complexes of DPG with the main-chain and side-chain PGI residues, which bind to it in the recognition site. We then consider DPG complexes with an increasing number of PGI residues. The largest QC complexes encompass the entirety of the recognition site, with six structural water molecules totaling up to 211 atoms. A persistent and satisfactory agreement could be shown between ΔE(SIBFA) and ΔE(QC). These validations constitute an essential first step toward large-scale molecular dynamics simulations of DPG-based biosensors bound at the PGI dimer interface. © 2020 Wiley Periodicals, Inc.     

Binding of 5-phospho-D-arabinonohydroxamate and 5-phospho-D-arabinonate inhibitors to zinc phosphomannose isomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics

Type I phosphomannose isomerase (PMI) is a Zn-dependent metalloenzyme involved in the isomerization of D-fructose 6-phosphate to D-mannose 6-phosphate. One of our laboratories has recently designed and synthesized 5-phospho-D-arabinonohydroxamate (5PAH), an inhibitor endowed with a nanomolar affinity for PMI (Roux et al., Biochemistry 2004, 43, 2926). By contrast, the 5-phospho-D-arabinonate (5PAA), in which the hydroxamate moiety is replaced by a carboxylate one, is devoid of inhibitory potency. Subsequent biochemical studies showed that in its PMI complex, 5PAH binds Zn(II) through its hydroxamate moiety rather than through its phosphate. These results have stimulated the present theoretical investigation in which we resort to the SIBFA polarizable molecular mechanics procedure to unravel the structural and energetical aspects of 5PAH and 5PAA binding to a 164-residue model of PMI. Consistent with the experimental results, our theoretical studies indicate that the complexation of PMI by 5PAH is much more favorable than by 5PAA, and that in the 5PAH complex, Zn(II) ligation by hydroxamate is much more favorable than by phosphate. Validations by parallel quantum-chemical computations on model of the recognition site extracted from the PMI-inhibitor complexes, and totaling up to 140 atoms, showed the values of the SIBFA intermolecular interaction energies in such models to be able to reproduce the quantum-chemistry ones with relative errors < 3%. On the basis of the PMI-5PAH SIBFA energy-minimized structure, we report the first hypothesis of a detailed view of the active site of the zinc PMI complexed to the high-energy intermediate analogue inhibitor, which allows us to identify active site residues likely involved in the proton transfer between the two adjacent carbons of the substrates.     

Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy

We present an overview of the SIBFA polarizable molecular mechanics procedure, which is formulated and calibrated on the basis of quantum chemistry (QC). It embodies nonclassical effects such as electrostatic penetration, exchange-polarization, and charge transfer. We address the issues of anisotropy, nonadditivity, and transferability by performing parallel QC computations on multimolecular complexes. These encompass multiply H-bonded complexes and polycoordinated complexes of divalent cations. Recent applications to the docking of inhibitors to Zn-metalloproteins are presented next, namely metallo-beta-lactamase, phosphomannoisomerase, and the nucleocapsid of the HIV-1 retrovirus. Finally, toward third-generation intermolecular potentials based on density fitting, we present the development of a novel methodology, the Gaussian electrostatic model (GEM), which relies on ab initio-derived fragment electron densities to compute the components of the total interaction energy. As GEM offers the possibility of a continuous electrostatic model going from distributed multipoles to densities, it allows an inclusion of short-range quantum effects in the molecular mechanics energies. The perspectives of an integrated SIBFA/GEM/QM procedure are discussed.     

Binding of D- and L-captopril inhibitors to metallo-beta-lactamase studied by polarizable molecular mechanics and quantum mechanics

The bacterial Zn2+ metallo-beta-lactamase from B. fragilis is a zinc-enzyme with two potential metal ion binding sites. It cleaves the lactam ring of antibiotics, thus contributing to the acquired resistance of bacteria against antibiotics. The present study bears on the binuclear form of the enzyme. We compare several possible binding modes of captopril, a mercaptocarboxamide inhibitor of several zinc-metalloenzymes. Two diastereoisomers of captopril were considered, with either a D- or an L-proline residue. We have used the polarizable molecular mechanics procedure SIBFA (Sum of Interactions Between Fragments ab initio computed). Two beta-lactamase models were considered, encompassing 104 and 188 residues, respectively. The energy balances included the inter and intramolecular interaction energies as well as the contribution from solvation computed using a continuum reaction field procedure. The thiolate ion of the inhibitor is binding to both metal ions, expelling the bridging solvent molecule from the uncomplexed enzyme. Different competing binding modes of captopril were considered, either where the inhibitor binds in a monodentate mode to the zinc cations only with its thiolate ion, or in bidentate modes involving additional zinc binding by its carboxylate or ketone carbonyl groups. The additional coordination by the inhibitor's carboxylate or carbonyl group always occurs at the zinc ion, which is bound by a histidine, a cysteine, and an aspartate side chain. For both diastereomers, the energy balances favor monodentate binding of captopril via S-. The preference over bidentate binding is small. The interaction energies were recomputed in model sites restricted to captopril, the Zn2+ cations, and their coordinating end side chains from beta-lactamase (98 atoms). The interaction energies and their ranking among competing arrangements were consistent with those computed by ab initio HF and DFT procedures.     

Quantum‐chemistry based calibration of the alkali metal cation series (Li+Cs+) for large‐scale polarizable molecular mechanics/dynamics simulations

The alkali metal cations in the series Li⁺? Cs⁺ act as major partners in a diversity of biological processes and in bioinorganic chemistry. In this article, we present the results of their calibration in the context of the SIBFA polarizable molecular mechanics/dynamics procedure. It relies on quantum‐chemistry (QC) energy‐decomposition analyses of their monoligated complexes with representative O? , N? , S? , and Se? ligands, performed with the aug‐cc‐pVTZ(‐f) basis set at the Hartree–Fock level. Close agreement with QC is obtained for each individual contribution, even though the calibration involves only a limited set of cation‐specific parameters. This agreement is preserved in tests on polyligated complexes with four and six O? ligands, water and formamide, indicating the transferability of the procedure. Preliminary extensions to density functional theory calculations are reported.     

Complexes of a Zn‐metalloenzyme binding site with hydroxamate‐containing ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown

Zn‐metalloproteins are a major class of targets for drug design. They constitute a demanding testing ground for polarizable molecular mechanics/dynamics aimed at extending the realm of quantum chemistry (QC) to very long‐duration molecular dynamics (MD). The reliability of such procedures needs to be demonstrated upon comparing the relative stabilities of competing candidate complexes of inhibitors with the recognition site stabilized in the course of MD. This could be necessary when no information is available regarding the experimental structure of the inhibitor–protein complex. Thus, this study bears on the phosphomannose isomerase (PMI) enzyme, considered as a potential therapeutic target for the treatment of several bacterial and parasitic diseases. We consider its complexes with 5‐phospho‐d ‐arabinonohydroxamate and three analog ligands differing by the number and location of their hydroxyl groups. We evaluate the energy accuracy expectable from a polarizable molecular mechanics procedure, SIBFA. This is done by comparisons with ab initio quantum‐chemistry (QC) calculations in the following cases: (a) the complexes of the four ligands in three distinct structures extracted from the entire PMI‐ligand energy‐minimized structures, and totaling up to 264 atoms; (b) the solvation energies of several energy‐minimized complexes of each ligand with a shell of 64 water molecules; (c) the conformational energy differences of each ligand in different conformations characterized in the course of energy‐minimizations; and (d) the continuum solvation energies of the ligands in different conformations. The agreements with the QC results appear convincing. On these bases, we discuss the prospects of applying the procedure to ligand‐macromolecule recognition problems. © 2016 Wiley Periodicals, Inc.     

Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: Bimetallic binding site and structured waters

The existence of a network of structured waters in the vicinity of the bimetallic site of Cu/Zn‐superoxide dismutase (SOD) has been inferred from high‐resolution X‐ray crystallography. Long‐duration molecular dynamics (MD) simulations could enable to quantify the lifetimes and possible interchanges of these waters between themselves as well as with a ligand diffusing toward the bimetallic site. The presence of several charged or polar ligands makes it necessary to resort to second‐generation polarizable potentials. As a first step toward such simulations, we benchmark in this article the accuracy of one such potential, sum of interactions between fragments Ab initio computed (SIBFA), by comparisons with quantum mechanics (QM) computations. We first consider the bimetallic binding site of a Cu/Zn‐SOD, in which three histidines and a water molecule are bound to Cu(I) and three histidines and one aspartate are bound to Zn(II). The comparisons are made for different His6 complexes with either one or both cations, and either with or without Asp and water. The total net charges vary from zero to three. We subsequently perform preliminary short‐duration MD simulations of 296 waters solvating Cu/Zn‐SOD. Six representative geometries are selected and energy‐minimized. Single‐point SIBFA and QM computations are then performed in parallel on model binding sites extracted from these six structures, each of which totals 301 atoms including the closest 28 waters from the Cu metal site. The ranking of their relative stabilities as given by SIBFA is identical to the QM one, and the relative energy differences by both approaches are fully consistent. In addition, the lowest‐energy structure, from SIBFA and QM, has a close overlap with the crystallographic one. The SIBFA calculations enable to quantify the impact of polarization and charge transfer in the ranking of the six structures. Five structural waters, which connect Arg141 and Glu131, are endowed with very high dipole moments (2.7–3.0 Debye), equal and larger than the one computed by SIBFA in ice‐like arrangements (2.7 D).     

Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds?

Halogenated compounds are gaining an increasing importance in medicinal chemistry and materials science. Ab initio quantum chemistry (QC) has unraveled the existence of a “sigma hole” along the C? X (X = F, Cl, Br, I) bond, namely, a depletion of electronic density prolonging the bond, concomitant with a build‐up on its sides, both of which are enhanced along the F < Cl < Br < I series. We have evaluated whether these features were intrinsically built‐in in an anisotropic, polarizable molecular mechanics (APMM) procedure such as SIBFA (sum of interactions between fragments ab initio computed). For that purpose, we have computed the interaction energies of fluoro‐, chloro‐, and bromobenzene with two probes: a divalent cation, Mg(II), and water approaching X through either one H or its O atom. This was done by parallel QC energy‐decomposition analyses (EDA) and SIBFA computations. With both probes, the leading QC contribution responsible for the existence of the sigma hole is the Coulomb contribution E_c. For all three halogenated compounds, and with both probes, the in‐ and out‐of‐plane angular features of E_c were closely mirrored by the SIBFA electrostatic multipolar contribution (E_MTP). Resorting to such a contribution thus dispenses with empirically‐fitted “extra”, off‐centered partial atomic charges as in classical molecular mechanics/dynamics. © 2013 Wiley Periodicals, Inc.     

Favorable pendant-amino metal chelation in VX nerve agent model systems

We have performed DFT computational studies [B3LYP, 6-31+G] to obtain metal ion coordination isomers of VX-Me [MeP(O)(OMe)(SCH2CH2NMe2)], a model of two of the most lethal nerve agents: VX [MeP(O)(OEt)(SCH2CH2N(iPr)2)] and Russian-VX [MeP(O)(OCH2CHMe2)(SCH2CH2N(Et)2)]. Our calculations involved geometry optimizations of the neutral VX-Me model as well as complexes with H+, Li+, Na+, K+, Be2+, Mg2+, and Ca2+ that yielded 2-8 different stable chelation modes for each ion that involved mainly mono- and bidentate binding. Importantly, our studies revealed that the [O(P),N] bidentate binding mode, long thought to be the active mode in differentiating the hydrolytic path of VX from other nerve agents, was the most stable for all ions studied here. Binding energy depended mainly on ionic size as well as charge, with binding energies ranging from 364 kcal mol(-1) for Be2+ to 33 kcal mol(-1) for K+. Furthermore, calculated NMR shifts for VX-Me correlate to experimental values of VX.     

Parallel ab initio and molecular mechanics investigation of polycoordinated Zn(II) complexes with model hard and soft ligands: Variations of binding energy and of its components with number and charges of ligands

In this study we compare the binding energies of polycoordinated complexes of Zn²⁺ within cavities composed of model “hard” (H₂O, OH⁻) or “soft” (CH₃SH, CH₃S⁻) ligands. Ab initio supermolecule computations are performed at the HF and MP2 levels using extended basis sets to determine the binding energies and their components as a function of: the number of ligands, ranging from three to six; the net charge of the cavity; and the “hard” versus “soft” character of the ligands. These ab initio computations are used to test the reliability of the SIBFA molecular mechanics procedure, originally formulated and calibrated on the basis of ab initio computations, for such charged systems. The SIBFA intermolecular interaction energies match the corresponding ab initio values using a coreless effective potential split‐valence basis set with a relative error of ≤3%. Extensions to binuclear Zn²⁺ complexes, such as those that occur in the Zn‐binding sites of Gal4 and β‐lactamase proteins, are performed to test the applicability of the methodology for such systems. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1011–1039, 2000     

Energetics of Zn2+ binding to a series of biologically relevant ligands: A molecular mechanics investigation grounded on ab initio self-consistent field supermolecular computations

Detailed investigations are performed of the binding energetics of Zn²⁺ to a series of neutral and anionic ligands making up the sidechains of amino acid residues of proteins, as well as ligands which can be involved in Zn²⁺ binding during enzymatic activation: imidazole, formamide, methanethiol, methanethiolate, methoxy, and hydroxy. The computations are performed using the SIBFA molecular mechanics procedure (SMM), which expresses the interaction energy under the form of four separate contributions related to the corresponding ab initio supermolecular ones: electrostatic, short-range repulsion, polarization, and charge transfer. Recent refinements to this procedure are first exposed. To test the reliability of this procedure in large-scale simulations of inhibitor binding to metalloenzyme cavities, we undertake systematic comparisons of the SMM results with those of recent large basis set ab initio self-consistent field (SCF) supermolecule computations, in which a decomposition of the total ΔE into its four corresponding components is done (N. Gresh, W. Stevens, and M. Krauss, J. Comp. Chem., 16 , 843, 1995). For each complex, the evolution of each individual SMM energy component as a function of radial and in- and out-of-plane angular variations of the Zn²⁺ position reproduces with good accuracy the behavior of the corresponding SCF term. Computations performed subsequently on di- and oligoligated complexes of Zn²⁺ show that the SIBFA molecular mechanics (SMM) functionals, E_pol and E_ct, closely account for the nonadditive behaviors of the corresponding second-order energy contributions determined from the ab initio SCF calculations on these complexes and their nonlinear dependence on the number of ligands. Thus, the total intermolecular interaction energies computed with this procedure reproduce, with good accuracy, the corresponding SCF ones without the need for additional, extraneous terms in the intermolecular potential of polyligated complexes of divalent cations. © 1995 by John Wiley & Sons, Inc.     

A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field

A supervised, semiautomated approach to force field parameter fitting is described and applied to the SIBFA polarizable force field. The I‐NoLLS interactive, nonlinear least squares fitting program is used as an engine for parameter refinement while keeping parameter values within a physical range. Interactive fitting is shown to avoid many of the stability problems that frequently afflict highly correlated, nonlinear fitting problems occurring in force field parametrizations. The method is used to obtain parameters for the H₂O, formamide, and imidazole molecular fragments and their complexes with the Mg²⁺ cation. Reference data obtained from ab initio calculations using an auc‐cc‐pVTZ basis set exploit advances in modern computer hardware to provide a more accurate parametrization of SIBFA than has previously been available. © 2014 Wiley Periodicals, Inc.     

Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF

To account for the distortion of the coordination sphere that takes place in complexes containing open-shell metal cations such as Cu(II), we implemented, in sum of interactions between fragments ab initio computed (SIBFA) molecular mechanics, an additional contribution to take into account the ligand field splitting of the metal d orbitals. This term, based on the angular overlap model, has been parameterized for Cu(II) coordinated to oxygen and nitrogen ligands. The comparison of the results obtained from density functional theory computations on the one hand and SIBFA or SIBFA-LF on the other shows that SIBFA-LF gives geometric arrangements similar to those obtained from quantum mechanical computations. Moreover, the geometric improvement takes place without downgrading the energetic agreement obtained from SIBFA. The systems considered are Cu(II) interacting with six water molecules, four ammonia or four imidazoles, and four water plus two formate anions.     

Importance of explicit smeared lone‐pairs in anisotropic polarizable molecular mechanics. Torture track angular tests for exchange‐repulsion and charge transfer contributions

A correct representation of the short‐range contributions such as exchange‐repulsion (E _rep) and charge‐transfer (E _ct) is essential for the soundness of separable, anisotropic polarizable molecular mechanics potentials. Within the context of the SIBFA procedure, this is aimed at by explicit representations of lone pairs in their expressions. It is necessary to account for their anisotropic behaviors upon performing not only in‐plane, but also out‐of‐plane, variations of a probe molecule or cation interacting with a target molecule or molecular fragment. Thus, E _rep and E _ct have to reproduce satisfactorily the corresponding anisotropies of their quantum chemical (QC) counterparts. A significant improvement of the out‐of‐plane dependencies was enabled when the sp² and sp localized lone‐pairs are, even though to a limited extent, delocalized on both sides of the plane, above and below the atom bearer but at the closely similar angles as the in‐plane lone pair. We report calibration and validation tests on a series of monoligated complexes of a probe Zn(II) cation with several biochemically relevant ligands. Validations are then performed on several polyligated Zn(II) complexes found in the recognition sites of Zn‐metalloproteins. Such calibrations and validations are extended to representative monoligated and polyligated complexes of Mg(II) and Ca(II). It is emphasized that the calibration of all three cations was for each ΔE contribution done on a small training set bearing on a limited number of representative N , O , and S monoligated complexes. Owing to the separable nature of ΔE , a secure transferability is enabled to a diversity of polyligated complexes. For these the relative errors with respect to the target ΔE (QC) values are generally < 3%. Overall, the article proposes a full set of benchmarks that could be useful for force field developers. © 2017 Wiley Periodicals, Inc.     

Many-body exchange-repulsion in polarizable molecular mechanics. I. Orbital-based approximations and applications to hydrated metal cation complexes

We have quantified the extent of the nonadditivity of the short-range exchange-repulsion energy, E(exch-rep), in several polycoordinated complexes of alkali, alkaline-earth, transition, and metal cations. This was done by performing ab initio energy decomposition analyses of interaction energies in these complexes. The magnitude of E(exch-rep(n-body, n > 2)) was found to be strongly cation-dependent, ranging from close to zero for some alkali metal complexes to about 6 kcal/mol for the hexahydrated Zn(2+) complex. In all cases, the cation-water molecules, E(exch-rep(three-body)), has been found to be the dominant contribution to many-body exchange-repulsion effects, higher order terms being negligible. As the physical basis of this effect is discussed, a three-center exponential term was introduced in the SIBFA (Sum of Interactions Between Fragments Ab initio computed) polarizable molecular mechanics procedure to model such effects. The three-body correction is added to the two-center (two-body) overlap-like formulation of the short-range repulsion contribution, E(rep), which is grounded on simplified integrals obtained from localized molecular orbital theory. The present term is computed on using mostly precomputed two-body terms and, therefore, does not increase significantly the computational cost of the method. It was shown to match closely E(three-body) in a series of test cases bearing on the complexes of Ca(2+), Zn(2+), and Hg(2+). For example, its introduction enabled to restore the correct tetrahedral versus square planar preference found from quantum chemistry calculations on the tetrahydrate of Hg(2+) and [Hg(H(2)O)(4)](2+).     

Capillary electrophoretic separation and computational modeling of inclusion complexes of β‐cyclodextrin and 18‐crown‐6 ether with primaquine and quinocide

The antimalarial drug primaquine (PQ) and its contaminant, the positional isomer quinocide (QC) have been successfully separated using capillary electrophoresis with either β‐cyclodextrin (β‐CD) or 18‐crown‐6 ether (18C6) as chiral mobile phase additive. The interactions of the drugs with cyclodextrins and 18C6 were studied by the semiempirical method (Parametric Model 3) PM3. Theoretical calculations for the inclusion complexes of PQ and QC with α‐CD, β‐CD and 18C6 were performed. Data from the theoretical calculations are correlated and discussed with respect to the electrophoretic migration behavior. More stable complexes are predicted for the PQ–β‐CD and PQ–18C6 complexes. The coelution of PQ and QC when α‐CD was used as buffer additive can be explained by their comparable stabilities of the inclusion complex formed, while significant differences in the complexation stabilities of the drugs with β‐CD is responsible for their separation. The stronger hydrogen bonding in PQ–18C6 system is responsible for the separation between PQ and QC when 18C6 was used as chiral mobile phase additive. Copyright © 2009 John Wiley & Sons, Ltd.     

Bridged bis(beta-cyclodextrin)s possessing coordinated metal center(s) and their inclusion complexation behavior with model substrates: enhanced molecular binding ability by multiple recognition.

To investigate quantitatively the cooperative binding ability of several beta-cyclodextrin oligomers bearing single or multiligated metal center(s), the inclusion complexation behavior of four bis(beta-cyclodextrin)s (2-5) linked by 2,2'-bipyridine-4,4'-dicarboxy tethers and their copper(II) complexes (6-9) with representative dye guests, i.e., methyl orange (MO), acridine red (AR), rhodamine B (RhB), ammonium 8-anilino-1-naphthalenesulfonic acid (ANS), and sodium 6-(p-toludino)-2-naphthalenesulfonate (TNS), have been examined in aqueous solution at 25 degrees C by means of UV-vis, circular dichroism, fluorescence, and 2D NMR spectroscopy. The results obtained indicate that bis(beta-cyclodextrin)s 2-5 can associate with one or three copper(II) ion(s) producing 2:1 or 2:3 bis(beta-cyclodextrin)-copper(II) complexes. These metal-ligated oligo(beta-cyclodextrin)s can bind two model substrates to form intramolecular 2:2 host-guest inclusion complexes and thus significantly enhance the original binding abilities of parent beta-cyclodextrin and bis(beta-cyclodextrin) toward model substrates through the cooperative binding of two guest molecules by four tethered cyclodextrin moieties, as well as the additional binding effect supplied by ligated metal center(s). Host 6 showed the highest enhancement of the stability constant, up to 38.3 times for ANS as compared with parent beta-cyclodextrin. The molecular binding mode and stability constant of substrates by bridged bis- and oligo(beta-cyclodextrin)s 2-9 are discussed from the viewpoint of the size/shape-fit interaction and molecular multiple recognition between host and guest.     

Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations

We present refinements of the SIBFA molecular mechanics procedure to represent the intermolecular interaction energies of Zn(II). The two first-order contributions, electrostatic (E(MTP)), and short-range repulsion (E(rep)), are refined following the recent developments due to Piquemal et al. (Piquemal et al. J Phys Chem A 2003, 107, 9800; and Piquemal et al., submitted). Thus, E(MTP) is augmented with a penetration component, E(pen), which accounts for the effects of reduction in electronic density of a given molecular fragment sensed by another interacting fragment upon mutual overlap. E(pen) is fit in a limited number of selected Zn(II)-mono-ligated complexes so that the sum of E(MTP) and E(pen) reproduces the Coulomb contribution E(c) from an ab initio Hartree-Fock energy decomposition procedure. Denoting by S, the overlap matrix between localized orbitals on the interacting monomers, and by R, the distance between their centroids, E(rep) is expressed by a S(2)/R term now augmented with an S(2)/R(2) one. It is calibrated in selected monoligated Zn(II) complexes to fit the corresponding exchange repulsion E(exch) from ab initio energy decomposition, and no longer as previously the difference between (E(c) + E(exch)) and E(MTP). Along with the reformulation of the first-order contributions, a limited recalibration of the second-order contributions was carried out. As in our original formulation (Gresh, J Comput Chem 1995, 16, 856), the Zn(II) parameters for each energy contribution were calibrated to reproduce the radial behavior of its ab initio HF counterpart in monoligated complexes with N, O, and S ligands. The SIBFA procedure was subsequently validated by comparisons with parallel ab initio computations on several Zn(II) polyligated complexes, including binuclear Zn(II) complexes as in models for the Gal4 and beta-lactamase metalloproteins. The largest relative error with respect to the RVS computations is 3%, and the ordering in relative energies of competing structures reproduced even though the absolute numerical values of the ab initio interaction energies can be as large as 1220 kcal/mol. A term-to-term identification of the SIBFA contributions to their ab initio counterparts remained possible even for the largest sized complexes.     

Comparative binding energetics of Mg2+, Ca2+, Zn2+, and Cd2+ to biologically relevant ligands: Combined ab initio SCF supermolecule and molecular mechanics investigation

A combined ab initio SCF supermolecule and molecular mechanics investigation is carried out on the binding energetics of the divalent cations Mg²⁺, Ca²⁺, Zn²⁺, and Cd²⁺ to a series of the most common ligand functional groups found in biomolecules. The SCF binding energy components are resolved using the restricted variational space method.¹ The results show that the SIBFA molecular mechanics (SMM) procedure² reproduces the ab initio binding energies and total energy variations as a function of intermolecular variables. The model also reproduces the selectivity energetics for exchange reactions. Thus, the SMM procedure can be used without reparametrization to describe the coordination energetics of complex molecules including those subject to coordination changes. The energetic properties of divalent cation-hexahydrate complexes are compared as examples of a complete, realistic coordination system. The hexahydrates exhibit strong nonadditive effects typical of dication coordination. Nevertheless, these energetics are satisfactorily reproduced by the SMM procedure. © 1996 John Wiley & Sons, Inc.     

Chiral discrimination asserted by enantiomers of Ni (II), Cu (II) and Zn (II) Schiff base complexes in DNA binding, antioxidant and antibacterial activities

Chiral Schiff base ligands (S)-H(2)L and (R)-H(2)L and their complexes (S-Ni-L, R-Ni-L, S-Cu-L, R-Cu-L, S-Zn-L and R-Zn-L) were synthesized, characterized and examined for their DNA binding, antioxidant and antibacterial activities. The complexes showed higher binding affinity to calf thymus DNA with binding constant ranging from 2.0×10(5) to 4.5×10(6) M(-1). All the complexes also exhibited remarkable superoxide (56-99%) and hydroxyl scavenging (45-89%) activities as well as antibacterial activities against gram (+) and gram (-) bacteria. However, none of the complexes showed antifungal activity. Conclusively, S enantiomers of the complexes were found to be relatively more efficient for DNA interaction, antioxidant and antibacterial activities than their R enantiomers. This study reveals the possible utilization of chiral Schiff base complexes for pharmaceutical applications.