Stability Of Various Conformations Research Articles

Complexity of the Role of Various Site-Specific and Selective Sudlow Binding Site Drugs in the Energetics and Stability of the Acridinedione Dye-Bovine Serum Albumin Complex: A Molecular Docking Approach.

Molecular docking (Mol.Doc) techniques were employed to ascertain the binding affinity of two resorcinol-based acridinedione dyes (ADR1 and ADR2) with the widely studied globular protein Bovine Serum Albumin (BSA) in the presence of site-selective binding drugs by Autodock Vina 4.2 software. Docking of various feasible conformers of ADR1 dye with BSA was found to be energetically more favored than ADR2 dye, even though both these dyes differ in the 9th position of the basic dye structure. Analysis of dyes with BSA establishes the location of dye in all of the binding sites of BSA, predominantly through conventional and nonconventional hydrogen-bonding (HB) interactions. The coexistence of hydrophobic interactions resulted in the stability of various conformers generated. The introduction of site I and site II (Sudlow site binding drugs) into ADR1-BSA and ADR2-BSA complexes effectively destabilizes the dye-protein complex; however, the drugs do not displace ADR dyes completely from their selective binding domains. Site II binding drugs effectively destabilize the binding ability of the dye-protein complex rather than site I drugs. However, docking of site I drug 3-carboxyl-4-methyl-5-propyl-2-furanpropanic acid (CMPF) largely destabilizes the ADR1-protein complex, whereas indomethacin (INDO) enhances the binding affinity of the ADR2-protein complex. Interestingly, simultaneous docking of ADR dyes to the BSA-drug complex results in larger stability of the protein-drug complex through HB interactions rather than hydrophobic interactions. Both ADR1 and ADR2 dyes predominantly occupy the Sudlow binding sites of BSA, and the introduction of either site I or site II binding drugs does not displace the dye efficiently from the corresponding binding sites, rather the drugs are effectively displaced toward other binding domains apart from their specific site-binding domains of BSA. Through Mol.Doc techniques, we authenticate that the interactions in host-guest complex systems involving competing ligands are established in depth, wherein the dye as well as the amino acid (AA) moieties in BSA act as both HB donor and acceptor sites apart from several hydrophobic interactions coexisting toward the stability.

New promising generation of phosphates α-aminophosphonates: Design, synthesis, in-vitro biological evaluation and computational study

A novel category of phosphate-phosphonate compounds is synthesized by a sequence multicomponent reactions strategy of Kabachnik-Fields and Atherton-Todd reactions. All the designed products are obtained with good chemical yields in short reaction times, and confirmed by spectroscopy analyses. The diethyl [(4-diethylphosphate phenyl) (4-trifluoromethyl phenylamino) methyl] phosphonate 6g is characterized by single-crystal X-ray analysis. These compounds exhibited a strong antifungal effect, a low inhibition of AChE, and no inhibitory activity on BChE, with interesting antioxidant capacity. Results make them promising candidates as original organophosphorus pesticides. The DFT calculations concerning relative stability of various conformers, besides the comparison of the measured and calculated NMR spectra of selected compounds; suggest that conformational interconversion can quite easily occur in this type of molecules, so that many structures of the same compound can coexist in solution.

Local energy decomposition analysis of hydrogen-bonded dimers within a domain-based pair natural orbital coupled cluster study.

The local energy decomposition (LED) analysis allows for a decomposition of the accurate domain-based local pair natural orbital CCSD(T) [DLPNO-CCSD(T)] energy into physically meaningful contributions including geometric and electronic preparation, electrostatic interaction, interfragment exchange, dynamic charge polarization, and London dispersion terms. Herein, this technique is employed in the study of hydrogen-bonding interactions in a series of conformers of water and hydrogen fluoride dimers. Initially, DLPNO-CCSD(T) dissociation energies for the most stable conformers are computed and compared with available experimental data. Afterwards, the decay of the LED terms with the intermolecular distance (r) is discussed and results are compared with the ones obtained from the popular symmetry adapted perturbation theory (SAPT). It is found that, as expected, electrostatic contributions slowly decay for increasing r and dominate the interaction energies in the long range. London dispersion contributions decay as expected, as r−6. They significantly affect the depths of the potential wells. The interfragment exchange provides a further stabilizing contribution that decays exponentially with the intermolecular distance. This information is used to rationalize the trend of stability of various conformers of the water and hydrogen fluoride dimers.

An Organic Receptor Isolated in an Unusual Intermediate Conformation: Computation, Crystallography, and Hirshfeld Surface Analysis.

1,1″-1,4-Phenylene-bis(methylene)bis-4,4'-bipyridinium cation [C28H24N4]2+ (c), an organic receptor that generally crystallizes in its anti conformation, has recently been shown to be isolated in its syn conformation in an ion-paired compound [C28H24N4][Zn(dmit)2]·2DMF (dmit2- = 1,3-dithiole-2-thione-4,5-dithiolate; DMF = dimethylformamide). In this article, we demonstrated that the same receptor [C28H24N4]2+ (c) can also be stabilized in an unusual intermediate conformation (neither syn nor anti) with PF6- anion in compound [C28H24N4](PF6)2·(1,4-dioxane) (1·(1,4-dioxane)). The energetically favored anti conformation has been described in its nitrate salt [C28H24N4](NO3)2·2H2O (2·2H2O). Compounds 1·(1,4-dioxane) and 2·2H2O, crystallizing in triclinic and monoclinic systems with space groups P1̅ and P21/n, respectively, were additionally characterized by Hirshfeld surface analysis. The density functional theory calculations are performed to understand the internal mechanism of the stability of various conformers of cationic receptor c, compound 1, and compound 2. In conjunction with the electronic stability of the conformers, the natural bond orbital analysis and conformational equilibrium constants at different temperatures are also calculated to find out the sources of the different stability of the various conformers of experimentally synthesized compounds.

Identification of potential inhibitors for oncogenic target of dihydroorotate dehydrogenase using in silico approaches

Dihydroorotate dehydrogenase (DHODH) plays a major role in the rate limiting step of de novo pyrimidine biosynthesis pathway and it is pronounced as a novel target for drug development of cancer. The currently available drugs against DHODH are ineffective and bear various side effects. Three-dimensional structure of the targeted protein was constructed using molecular modeling approach followed by 100 ns molecular dynamics simulations. In this study, High Throughput Virtual Screening (HTVS) was performed using various compound libraries to identify pharmacologically potential molecules. The top four identified lead molecules includes NCI_47074, HitFinder_7630, Binding_66981 and Specs_108872 with high docking score of −9.45, -8.29, -8.04 and −8.03 kcal/mol and the corresponding binding free energy were −16.25, -56.37, -26.93 and −48.04 kcal/mol respectively. Arg122, Arg185, Glu255 and Gly257 are the key residues found to be interacting with the ligands. Molecular dynamics simulations of DHODH-inhibitors complexes were performed to assess the stability of various conformations from complex structures of TtDHODH. Furthermore, stereoelectronic features of the ligands were explored to facilitate charge transfer during the protein-ligand interactions using Density Functional Theoretical approach. Based on in silico analysis, the ligand NCI_47074 ((2Z)-3-({6-[(2Z)-3-carboxylatoprop-2-enamido]pyridin-2-yl}carbamoyl)prop-2-enoate) was found to be the most potent lead molecule which was validated using energetic and electronic parameters and it could serve as a template for designing effective anticancerous drug molecule.

Intermolecular interactions between molecules in various conformational states: the dimer of oxalic acid.

We considered stability of the dimer of oxalic acid. The global minimum energy structure identified by us is stabilized by two inter- and four intramolecular hydrogen bonds, whereas the most stable structure identified in previous studies is supported by two inter- and three intramolecular hydrogen bonds. The latter structure proves to be less stable by 25 meV than the former. The global minimum stability results from a balancing act between a moderately attractive two-body interaction energy and small repulsive one-body terms. We have analyzed zero-point vibrational corrections to the stability of various conformers of oxalic acid and their dimers. We have found that minimum energy structures with the most stabilizing sets of hydrogen bonds have the largest zero-point vibrational energy, contrary to a naive anticipation based on red shifts of OH stretching modes involved in hydrogen bonds.

2-Acylamino- and 2,4-Bis(acylamino)pyrimidines as Supramolecular Synthons Analyzed by Multiple Noncovalent Interactions. DFT, X-ray Diffraction, and NMR Spectral Studies

Intermolecular interactions of ten 2-acylamino and 2,4-bis(acylamino)pyrimidines (7 of which are previously unknown) have been investigated by X-ray structural, quantum chemical (DFT), and NMR spectral methods. Especially the concentration dependencies of the (1)H NMR chemical shifts and titrations with other molecules capable of multiple hydrogen bonding provided useful information regarding their association via triple or quadruple hydrogen bonding, which is controlled by the conformational preferences of 2-acylamino- and 2,4-bis(acylamino)pyrimidines. On comparison of the properties of 2-acylamino- and 2,4-bis(acylamino)pyrimidines with the corresponding pyridines, an additional nitrogen in the heterocyclic ring is the crucial factor in explaining the stability of various conformers and dimers of pyrimidines. Computational modeling of their dimerization (self-association) and heteroassociation supports the experimental findings. The substituent effects in 2-acylamino- and 2,4-bis(acylamino)pyrimidines are discussed via inter- and intramolecular terms. The subtle balance between several structural factors and their influence on the aggregation of studied pyrimidines was confirmed also by variable-temperature NMR and NOE experiments. X-ray structures of 2-methyl- and 2-adamantyl-CONH-pyrimidines revealed very different intermolecular interactions, showing the importance of the substituent size on the self-assembly process. As a whole NMR spectral, X-ray structural, and computational data of 2-acylamino- and 2,4-bis(acylamino)pyrimidines can be interpreted in terms of multiple intra-/intermolecular interactions.

A computational investigation and the conformational analysis of dimers, anions, cations, and zwitterions ofL‐phenylalanine

The structure and stability of various conformations of L-phenylalanine (PheN) and its zwitterions (PheZ), along with their ionized counterparts, cation (PheC) and anion (PheA), generated by adding and removing a proton respectively, have been investigated using first principle calculations in vacuum and in solution. This is followed by an extensive study on various possible dimer (PheD) conformations, which are noncovalently bound units without a peptide bond. This study results in 52, 31, 12, 9, and 11 minimum energy structures on the potential energy surfaces of PheD, PheN, PheC, PheA, and PheZ, respectively. Several important nonbonded interactions such as hydrogen bonds, NH-π, CH-π, OH-π, and π-π interactions, which impart stability to the monomeric and dimeric units, have been analyzed. The capability and strength of the nonbonded interactions drastically changing the conformational orientations of monomeric units has been illustrated.

Model-Based Thermodynamic Analysis of Reversible Unfolding Processes

Folding and unfolding of many biological macromolecules can be characterized thermodynamically, yielding a wealth of information about the stability of various conformations and the interactions that hold them together. The relevant thermodynamic parameters are usually obtained by employing spectroscopic and/or calorimetric techniques and fitting an appropriate thermodynamic model to the experimental data. In this work, we compare the traditional approach of fitting the thermodynamic model to experimental data obtained from each experiment individually and the global approach of simultaneously fitting the model to all available data from different experiments. On the basis of several specific examples of DNA and protein unfolding, we demonstrate that piece-by-piece verification of the proposed thermodynamic model using individual fits is frequently inappropriate and can result in an incorrect mechanism and thermodynamics of the studied unfolding process. We find that while the two approaches are complementary in some aspects of analysis global fitting is essential for the appropriate selection and critical evaluation of the model mechanism. Only a good global fit thus gives us confidence that the obtained thermodynamic parameters of unfolding have real physical meaning.

Modulation of KvAP Unitary Conductance and Gating by 1-Alkanols and Other Surface Active Agents

The actions of alcohols and anesthetics on ion channels are poorly understood. Controversy continues about whether bilayer restructuring is relevant to the modulatory effects of these surface active agents (SAAs). Some voltage-gated K channels (Kv), but not KvAP, have putative low affinity alcohol-binding sites, and because KvAP structures have been determined in bilayers, KvAP could offer insights into the contribution of bilayer mechanics to SAA actions. We monitored KvAP unitary conductance and macroscopic activation and inactivation kinetics in PE:PG/decane bilayers with and without exposure to classic SAAs (short-chain 1-alkanols, cholesterol, and selected anesthetics: halothane, isoflurane, chloroform). At levels that did not measurably alter membrane specific capacitance, alkanols caused functional changes in KvAP behavior including lowered unitary conductance, modified kinetics, and shifted voltage dependence for activation. A simple explanation is that the site of SAA action on KvAP is its entire lateral interface with the PE:PG/decane bilayer, with SAA-induced changes in surface tension and bilayer packing order combining to modulate the shape and stability of various conformations. The KvAP structural adjustment to diverse bilayer pressure profiles has implications for understanding desirable and undesirable actions of SAA-like drugs and, broadly, predicts that channel gating, conductance and pharmacology may differ when membrane packing order differs, as in raft versus nonraft domains.

Bond Dissociation Energies and Equilibrium Structures of Cu+(MeOH)x, x = 1−6, in the Gas Phase: Competition between Solvation of the Metal Ion and Hydrogen-Bonding Interactions

The solvation of Cu+ by methanol (MeOH) was studied via examination of the kinetic energy dependence of the collision-induced dissociation of Cu+(MeOH)x complexes, where x = 1-6, with Xe in a guided ion beam tandem mass spectrometer. In all cases, the primary and lowest-energy dissociation channel observed is the endothermic loss of a single MeOH molecule. The primary cross section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) after accounting for the effects of multiple ion-neutral collisions, kinetic and internal energy distributions of the reactants, and lifetimes for dissociation. Density functional theory calculations at the B3LYP/6-31G* level are performed to obtain model structures, vibrational frequencies, and rotational constants for the Cu+(MeOH)x complexes and their dissociation products. The relative stabilities of various conformations and theoretical BDEs are determined from single-point energy calculations at the B3LYP/6-311+G(2d,2p) level of theory using B3LYP/6-31G*-optimized geometries. The relative stabilities of the various conformations of the Cu+(MeOH)x complexes and the trends in the sequential BDEs are explained in terms of stabilization gained from sd hybridization, hydrogen-bonding interactions, electron donor-acceptor natural bond orbital stabilizing interactions, and destabilization arising from ligand-ligand repulsion.

Intramolecular nonbonding interactions in organoseleniums: Quantification using a computational thermochemical approach

Intramolecular Se⋯O nonbonding interactions in a series of ortho-formylarylselenides (O⋯Se–Y, with Y = –Me, –Ph, –CN, –Cl, and –F) are quantified using density functional theory. Two methods based on the relative stabilities of various conformers are employed in evaluating the strength of intramolecular interactions. These methods, namely, cis–trans (CT) and thermodynamic cycle (TDC), depends on the energy changes associated with conformational interconversion, where the nonbonding interaction is turned on or off (respectively, in cis and trans conformer). The strength of interactions are found to be dependent on the nature of Se–Y acceptor orbitals and follows the order Me ∼ Ph < CN < Cl < F. Natural Bond Orbital (NBO) analysis using DFT methods points to n O → σ Se – Y ∗ electron delocalization as the key contributing factor towards Se⋯O nonbonding interaction. Examination of the topological properties of the electron density with the Atoms-in-Molecule (AIM) method reveals that the electron density at the Se⋯O bond critical point exhibits a fairly good correlation with the nonbonding interaction energies estimated using the CT and TDC methods.

An ab initio quantum chemical study of cumulative double bonds: stability of various conformers and charge distribution analysis. Part I. XY 2H 2 hierarchy (X=O, S, Se and Y=N, P, As)

In this paper, various properties of XY 2H 2 (H–Y X Y–H) (X=O, S, Se and Y=N, P, As) hierarchy have been studied using ab initio quantum chemical methods. General geometrical tendencies have been observed for all members of this family as well as some distinguished geometrical characters of OP 2H 2 and OAs 2H 2 molecules. The energetic calculations reveal that in four molecules (SN 2H 2, SeN 2H 2, OP 2H 2 and OAs 2H 2), ZZ is the most stable conformer and EZ and EE stand on subsequent stability ranks. So it has been demonstrated that ZZ's unusual stability is not confined to sulfur diimides. The charge distribution analysis focusing on atomic partial charge distribution reveals that indeed a common property, namely significant charge separation takes place in the above-mentioned molecules. To characterize and stress on this ZZ's unusual and possibly unprecedented stability relative to EZ and EE, we have proposed the name ‘Z-effect’.

An ab initio investigation of sulfur diimides: stability of various conformers and conformational analysis part II. Dimethyl sulfur diimides (DMSD)

In this paper, various properties of dimethyl sulfur diimides (DMSD) as the simplest organic member of Sulfur diimide family have been considered with aid of B3LYP method and correlation consistent basis set hierarchies. According to these calculations EZ conformer is predicted to be the most stable isomer while ZZ conformer has the second rank. Comparison of experimental NMR spectra with theoretical calculations has been carried out and firm evidences have been offered in favor of ZZ presence in solution. The possible pathways for interconversion of EZ and ZZ conformers have been investigated and a pseudo-rotation mechanism has been introduced as the best candidate. Theoretical calculated activation energies are in good agreement with experimental data. Also, zwitterionic (–NS +–N −–) nature of DMSD has been established.

An ab initio investigation of sulfur diimides: stability of various conformers and conformational analysis Part I. parent sulfur diimide

In this paper various properties of parent sulfur diimides (PSD) as the simplest member of sulfur diimides family have been considered with aid of B3LYP method and correlation consistent basis set hierarchies. According to these calculations ZZ conformer is predicted to be the most stable conformer while the difference with EZ conformer is completely minute. Also comparison of experimental microwave spectra with theoretical calculations have been carried out and good agreement have been observed. The properties of EE conformer have also been anticipated although no experimental data exist for this conformer. The possible pathways for interconversion between different conformers have been investigated and a pseudo-rotation mechanism has been determined as the best candidate.

Theoretical study of the stability of myrsinone in vacuo and in solution

The stability of various conformers of myrsinone (2,3-dihydroxy-5-undecyl-1,4-benzoquinone) and its tautomer [2,3-dihydroxy-5-(undec-1-ene)-cyclohex-2-ene-1,4-dione] has been studied in vacuo and in solution on model systems with the long alkyl side chains replaced with ethyl and eth-1-ene groups, respectively. Ab initio Hartree–Fock (HF) calculations in vacuo and free-energy calculations either in chloroform or in water solution, in the framework of the polarizable continuum model, have been carried out on the 6-31G* optimized geometries obtained in vacuo and in solution (water or chloroform). The nature of the stationary points found was investigated using normal mode analysis. The energy gap between the two tautomeric forms turns out to be about 1.3 kcal/mol in vacuo and becomes about 0.3 kcal/mol in chloroform solution, whereas in water the second tautomer is favored by about 1.2 kcal/mol. The effect of second-order Moller–Plesset (MP2) correlation corrections has been considered on both the energy and the geometry of the tautomers in vacuo, whereas in solution only their effect on the energy was taken into account. The contribution to the stability in the gas phase and in solution of the intramolecular hydrogen bonds between the hydroxy hydrogen and the quinonoid oxygen is larger at the MP2 level than at the HF one. The directionality of the hydrogen bonds between the hydroxy groups affects considerably only the stability of the isomer with the exocyclic double bond. The computed chemical shifts for the two tautomers were compared to the experimental ones. In addition the solvation properties of 2,5-dihydroxy-3-ethyl-1,4-benzoquinone and of an ortho-quinonoid system were considered in order to evaluate the effect of the repulsion between vicinal hydroxy or quinonoid groups.

Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions

A combination of conformational search, energy minimization, and energetic evaluation using a continuum solvent treatment has been employed to study the stability of various conformations of the DNA fragment d(CGCAGAA)/d(TTCGCG) containing a single adenine bulge. The extra-helical (looped-out) bulge conformation derived from a published x-ray structure and intra-helical (stacked bulge base) model structures partially based on nuclear magnetic resonance (NMR) data were used as start structures for the conformational search. Solvent-dependent contributions to the stability of the conformations were calculated from the solvent exposed molecular surface area and by using the finite difference Poisson-Boltzmann approach. Three classes (I-III) of bulge conformations with calculated low energies can be distinguished. The lowest-energy conformations were found in class I, corresponding to structures with the bulge base stacked between flanking helices, and class II, composed of structures forming a triplet of the bulge base and a flanking base pair. All extra-helical bulge structures, forming class III, were found to be less stable compared with the lowest energy structures of class I and II. The results are consistent with NMR data on an adenine bulge in the same sequence context indicating an intra-helical or triplet bulge conformation in solution. Although the total energies and total electrostatic energies of the low-energy conformations show only relatively modest variations, the energetic contributions to the stability were found to vary significantly among the classes of bulge structures. All intra-helical bulge structures are stabilized by a more favorable Coulomb charge-charge interaction but destabilized by a larger electrostatic reaction field contribution compared with all extra-helical and most triplet bulge structures. Van der Waals packing interactions and nonpolar surface-area-dependent contributions appear to favor triplet class II structures and to a lesser degree also the intra-helical stacked bulge conformations. The large conformational variation found for class III conformers might add a favorable entropic contribution to the stability of the extra-helical bulge form.

Molecular thermodynamic model for Helix‐Helix docking and protein aggregation

AbstractThe formation of aggregates, rather than correctly folded polypeptide chains, is a pressing problem in biotechnology that has been difficult to approach quantitatively. The competition between folding and aggregation has been carefully analyzed for bovine growth hormone (bGH) and can be attributed to incorrect helix‐helix docking for this four‐helix bundle protein. An extended molecular thermodynamic model reported here represents Gibbs energy changes associated with intramolecular and intermolecular helix‐helix dockings occurring during protein folding and protein aggregation. The model incorporates (1) a semiempirical local composition Gibbs energy expression to account for the helix‐helix hydrophobic interactions, which favor helix‐helix docking and aggregation and (2) a Flory‐Huggins‐type Gibbs energy expression to describe the configurational entropy of the polypeptide backbone conformation, which favors disaggregation. For the folding and aggregation of bGH, the molecular thermodynamic model provides estimates for the Gibbs energies and thermodynamic stabilities of various conformations of bGH and qualitatively accounts for the competition between aggregation and productive folding. It also successfully describes the inhibition of aggregation found with peptides corresponding to bGH helical sequences and the effect of site‐directed mutagenesis.

Geometries and stabilities of various conformers of cyanomethylene and other HC 2N isomers

Geometrical structures of various conformers ( 1–10) in HC 2N were optimized by the QCISD (T) method with the D95 ** basis set. Relative stabilities of the singlet and triplet conformers were obtained using single-reference and multi-reference SDCI + Q methods with the general contraction scheme of the [5s3p2d1f(C and N)/3s2p1d (H)] basis set. We agree with the qualitative conclusions of Schaefer and Roos that triplet cyanomethylene is bent. The energy difference between the bent ( 1) and the linear ( 2) triplet conformers is 1.3 kcal/mol at the single-reference SDCI + Q level of theory, in good agreement with Schaefer's estimate (0.8 kcal/mol). At the 9-reference SDCI + Q level of theory using the natural orbitals obtained in the single-reference SDCI calculations the energy difference is 2.1 kcal/mol, slightly larger than Schaefer's value. The singlet conformer of a ring structure lies 8.8 kcal/mol above the most stable triplet-bent 1.

The anomeric and reverse anomeric effect. A simple energy decomposition model for acetals and protonated acetals

Geometry optimizations at the 6-31G** level were performed on various conformers of XHmCH2YHn and XHmCH2YHn+I+ (protonated), with X, Y = N, O. The resulting anomeric stabilization energies were decomposed into steric, electrostatic (lone pair – lone pair, lone pair – hydrogen), and electronic contributions. Using approximate values for steric and electrostatic terms, the electronic energy was determined to be about −2 kcal/mol for the anomeric effect to arise from O, and −2.5 kcal/mol if it arises from N. For protonated systems, an additional energy term for the reverse anomeric effect had to be added, having a value of −4 kcal/mol for O in OH-CH2-NH3+ and −5 kcal/mol for N in NH2C-H2-NH3+. The anomeric effect due to N drives NH2-CH2-OH2+ to a charge-dipole complex of the type NH2=CH2+… OH2. The energy parameters obtained have been applied to predict relative stabilities of various conformers of methanetriol, aminomethanediol, and protonated methanetriol, with good success.