Conformational Energy Research Articles

Peripheral chain length-dependent complex phase behaviour in C3-symmetric hexa-alkylated liquid crystals

ABSTRACTWe report the thermal and self-assembly properties of C3-symmetric liquid crystalline (LC) molecules consisting of a conformationally tunable triazole-based mesogen and six-fold alkyl chains. Unlike the LC compound (1) based on non-crystallisable octyl chains, 2 and 3, which have crystallisable dodecyl and tetradecyl chains, respectively, exhibit a cold crystallisation which only takes place under slow heating conditions (2°C/min). In contrast with the vertically interdigitated lamellar crystalline phase of 1, a laterally interdigitated bilayered lamellar structure driven by the crystallisation of the dodecyl or tetradecyl chains is observed in the cold crystallisation temperature range. In addition to their crystalline morphology, 2 and 3 show LC morphological behaviour distinct from that of 1, 2 and 3 exhibit a hexagonal columnar LC phase consisting of T-shaped conformers rather than the lamellar LC phase of 1. The morphological transformation from the lamellar (1) to the columnar phase (2 and 3) can be rationalised by the alleviation of the conformational energy of the longer alkyl chains. Consequently, the simple variation of alkyl chain length in the C3-symmetric LC system results in contrasting thermal and assembly properties in the crystalline and LC phases.

The multi-state energy landscape of the SAM-I riboswitch: A single-molecule Förster resonance energy transfer spectroscopy study.

RNA (ribonucleic acid) molecules are highly flexible biopolymers fluctuating at physiological temperatures among many different conformations that are represented by minima in a hierarchical conformational free energy landscape. Here we have employed single-molecule FRET (smFRET) to explore the energy landscape of the B. subtilis yitJ SAM-I riboswitch (RS). In this small RNA molecule, specific binding of an S-adenosyl-L-methionine (SAM) ligand in the aptamer domain regulates gene expression by inducing structural changes in another domain, the expression platform, causing transcription termination by the RNA polymerase. We have measured smFRET histograms over wide ranges of Mg2+ concentration for three RS variants that were specifically labeled with fluorescent dyes on different sites. In the analysis, different conformations are associated with discrete Gaussian model distributions, which are typically fairly broad on the FRET efficiency scale and thus can be extremely challenging to unravel due to their mutual overlap. Our earlier work on two SAM-I RS variants revealed four major conformations. By introducing a global fitting procedure which models both the Mg2+ concentration dependencies of the fractional populations and the average FRET efficiencies of the individual FRET distributions according to Mg2+ binding isotherms, we were able to consistently describe the histogram data of both variants at all studied Mg2+ concentrations. With the third FRET-labeled variant, however, we found significant deviations when applying the four-state model to the data. This can arise because the different FRET labeling of the new variant allows two states to be distinguished that were previously not separable due to overlap. Indeed, the resulting five-state model presented here consistently describes the smFRET histograms of all three variants as well as their variations with Mg2+ concentration. We also performed a triangulation of the donor position for two of the constructs to explore how the expression platform is oriented with respect to the aptamer.

Solvent Modulation of Aromatic Substituent Effects in Molecular Balances Controlled by CH-π Interactions.

CH-π aromatic interactions are ubiquitous in nature and are capable of regulating important chemical and biochemical processes. Solvation and aromatic substituent effects are known to perturb the CH-π aromatic interactions. However, the nature by which the two factors influence one another is relatively unexplored. Here we demonstrate experimentally that there is a quantitative correlation between substituent effects in CH-π interactions and the hydrogen-bond acceptor constants of the solvating molecule. The CH-π interaction energies were measured by the conformational study of a series of aryl-substituted molecular balances in which the conformational preferences depended on the relative strengths of the methyl and aryl CH-π interactions in the folded and unfolded states, respectively. Due to the favorable methyl-aromatic interactions, the balances were found to exist predominantly in the folded state. The observed substituent effect in the conformational preferences of the balances was controlled by the explicit solvation/desolvation of the aryl proton. The interpretation of the conformational free energy as a function of substituents and solvation using Hunter's solvation model revealed that a linear relationship exists between the sensitivity of aromatic substituent effects (i.e., the ρ values derived from Hammett plots) and the hydrogen-bond acceptor propensity (βs) of the solvent molecule: ρ = 0.06βs - 0.04.

Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings.

Understanding of protein conformational dynamics is essential for elucidating molecular origins of protein structure-function relationship. Traditionally, reaction coordinates, i.e., some functions of protein atom positions and velocities have been used to interpret the complex dynamics of proteins obtained from experimental and computational approaches such as molecular dynamics simulations. However, it is nontrivial to identify the reaction coordinates a priori even for small proteins. Here, we evaluate the power of evolutionary couplings (ECs) to capture protein dynamics by exploring their use as reaction coordinates, which can efficiently guide the sampling of a conformational free energy landscape. We have analyzed 10 diverse proteins and shown that a few ECs are sufficient to characterize complex conformational dynamics of proteins involved in folding and conformational change processes. With the rapid strides in sequencing technology, we expect that ECs could help identify reaction coordinates a priori and enhance the sampling of the slow dynamical process associated with protein folding and conformational change.

Synthesis, anticancer assessment on human breast, liver and colon carcinoma cell lines and molecular modeling study using novel pyrazolo[4,3-c]pyridine derivatives

The key intermediate 3-aminopyrazolo[4,3-c]pyridine-4,6-dione (2) is considered as a precursor for some novel pyrazolo[4,3-c]pyridines 4a-c, arylhydrazopyrazolo[4,3-c]pyridines 8a-e, pyrazolo[4,5,1-ij][1,6]naphthyridines 11a-e and pyrido[4′,3′:3,4]pyrazolo[1,5-a]-pyrimidines 15a-d through Knovenegal condensation, coupling reaction and Michael addition. Some of the newly synthesized pyrazolo[4,3-c]pyridine derivatives were investigated for anticancer activity. The results of the cytotoxic activity revealed that compound 6b was the most active compound against the breast and liver carcinoma cell lines which gives IC50 values of 1.937 and 3.695 µg/mL, respectively compared to reference drug (doxorubicin) with IC50 values of 2.527 and 4.749 µg/ml, respectively. Moreover, compound 6c was potent compound against the colon carcinoma cell line which gives the value of IC50 = 2.914 µg/ml compared to doxorubicin with IC50 value of 3.641 µg/ml. Some selected of the novel synthesized compounds were docked inside the active site of ERK2 enzyme and were found display a suitable binding with the active site amino acids according to their bond lengths, angles and conformational energy.

Trans–cis isomerization energies of azopyridines: a calorimetric and computational study

Azobenzenes undergo reversible trans–cis photo-isomerization and have been studied extensively as photo-responsive materials. Despite their similar photochemistry, azopyridines have received relatively little attention; for example, their isomerization energies are presently unknown. In comparison with azobenzenes, azopyridines offer additional opportunities for materials design through hydrogen bonding and coordination chemistry. Here we report the isomerization energies for all three symmetrical azopyridines (i.e., the 2,2′-, 3,3′-, and 4,4′-isomers) through a combined experimental and computational study. Heat of isomerization was measured in the liquid state, with o-terphenyl introduced to suppress crystallization. We obtain ∆Eiso = 25.2 ± 0.6, 42.6 ± 0.6, and 35.0 ± 1.8 kJ mol−1 for 2,2′, 3,3′, and 4,4′-azopyridine, respectively. For azobenzene, we obtain ∆Eiso = 47.0 ± 1.3 kJ mol−1, in agreement with the literature value and validating our method. Theoretical calculations yielded gas-phase ∆Eiso in reasonable agreement with experiment and explain the low isomerization energy of 2,2′-azopyridine on the basis of a low-energy cis conformer. Because of the smaller van der Waals volume of the pyridine N relative to the phenyl CH, the two aromatic rings in the cis isomer can approach closer to coplanarity, leading to greater π-conjugation and lower conformational energy.

Synthesis of Flake-shaped [3]Cyclo-4,6-dibenzofuranylene

The cyclic trimer of dibenzofuran linked at the 4,6-positions, named [3]cyclo-4,6-dibenzofuranylene, was synthesized by Ni(0)-mediated reductive coupling of 4,6-dibromodibenzofuran. DFT calculation indicated that the flake-shaped C2 symmetric structure is the most stable conformer and the propeller-shaped D3 symmetric structure is the minor conformer with a higher energy (+19.1 kcal mol−1). The calculated inversion energy of the C2 conformer through a Cs symmetric transition state was +4.1 kcal mol−1, showing rapid fluctuation, which is consistent with the observation of only one set of 1H NMR signals of dibenzofuran of [3]cyclo-4,6-dibenzofuranylene.

Atom Types Independent Molecular Mechanics Method for Predicting the Conformational Energy of Small Molecules.

We previously implemented a well-known qualitative chemical principle into an accurate quantitative model computing relative potential energies of conformers. According to this principle, hyperconjugation strength correlates with electronegativity of donors and acceptors. While this earlier version of our model applies to σ bonds, lone pairs, disregarded in this earlier version, also have a major impact on the conformational preferences of molecules. Among the well-established principles used by organic chemists to rationalize some organic chemical behaviors are the anomeric effect, the alpha effect, basicity, and nucleophilicity. These effects are directly related to the presence of lone pairs. We report herein our effort to incorporate lone pairs into our model to extend its applicability domain to any saturated small molecules. The developed model H-TEQ 2 has been validated on a wide variety of molecules from polyaromatic molecules to carbohydrates and molecules with high heteroatoms/carbon ratios. Interestingly, this method, in contrast to common force field-based methods, does not rely on atom types and is virtually applicable to any organic molecules.

An improved two-rotor function for conformational potential energy surfaces of 20 amino acid diamides

Predicting the three-dimensional structure of a protein from its amino acid sequence requires a complete understanding of the molecular forces that influences the protein folding process. Each possible conformation has its corresponding potential energy, which characterizes its thermodynamic stability. This is needed to identify the primary intra- and inter-molecular interactions, so that we can reduce the dimensionality of the problem, and create a relatively simple representation of the system. Investigating this problem using quantum chemical methods produces accurate results; however, this also entails large computational resources. In this study, an improved two-rotor potential energy function is proposed to represent the backbone interactions in amino acids through a linear combination of a Fourier series and a mixture of Gaussian functions. This function is applied to approximate the 20 amino acid diamide Ramachandran-type PESs, and results yielded an average RMSE of 2.36 kJ mol−1, which suggest that the mathematical model precisely captures the general topology of the conformational potential energy surface. Furthermore, this paper provides insights on the conformational preferences of amino acid diamides through local minima geometries and energy ranges, using the improved mathematical model. The proposed mathematical model presents a simpler representation that attempts to provide a framework on building polypeptide models from individual amino acid functions, and consequently, a novel method for rapid but accurate evaluation of potential energies for biomolecular simulations.

In Silico Studies of Crystal Structure of HCV NS5B Polymerase and Inhibitor Complex

Quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics simulations were performed to study the hydrogen bonding and polar interactions of an inhibitor namely 2-{[(5- bromothiophen-2-yl) sulfonyl] amino}- 4-chlorobenzoic acid with HCV NS5B polymerase. Using the initial poses, our aim is to identify the minimum energy positions and calculate binding affinities of inhibitor to HCV. Results suggest that the accuracy of binding affinity prediction can be significantly affected by the proper treatment of the hydrogen bonding and polar interactions. Using this protocol, we successfully identified important poses of low RMSD with respect to crystallographic structure from the initially docked poses. This work shows that the most important energetic component contributing to binding for this particular protein-ligand system is the conformational energy. In addition, formation of hydrogen bonds can produce favorable van der Waals interactions with some important residues. This systematic study can provide guidance for the choice of QM/MM MD methods and design of new inhibitors targeting HCV.

Predicting structural and energetic changes in Met-aromatic motifs on methionine oxidation to the sulfoxide and sulfone.

Noncovalent interactions between Met and aromatic residues define a common Met-aromatic motif in proteins. Met oxidation to MetOn (n = 1 sulfoxide, n = 2 sulfone) alters protein stability and function. To predict the chemical and physical consequences of such oxidations, we modeled the chemistry and redox properties of MetOn-aromatic complexes in depth for comparison with our Met-aromatic models (E. A. Orabi and A. M. English, J. Phys. Chem. B, 2018, 122, 3760). We describe here ab initio quantum mechanical calculations at the MP2(full)/6-311++G(d,p) level of theory on complexes of MetOn (n = 1, 2; modeled by Me2SO and Me2SO2) with models of the side-chains of Phe (benzene, toluene), Trp (indole, 3-methylindole), Tyr (phenol, 4-methylphenol) and His (imidazole, 4-methylimidazole). Binding energies of the global minimum conformers (-3.4 to -11.9 kcal mol-1) indicate that the gas-phase Me2SOn-aromatics are 40-115% more stable than the Me2S-aromatics. Binding of S between the edge and face of the aromatic ring is favored in most complexes as it accommodates both robust σ- and π-type H-bonding. Interactions involving the σ-holes on the S atoms (σ-holeπar and σ-holeNar/Oar), as well as Sπ interactions in the sulfoxides, contribute to complex stability. Complexation modulates the ionization potential (IP) of the interacting fragments with the binding geometry dictating the center oxidized in the Me2SO-aromatics whereas the aromatic is oxidized in the Me2SO2 complexes because of the sulfone's high IP. Potentials of mean force reveal binding free energies of -0.2 to -0.7 kcal mol-1 in bulk water, which indicates that the Me2SOn-aromatics are up to 80% less stable than the corresponding aqueous Me2S-aromatics. Molecular dynamics simulations predict that Me2SOn preferentially interacts with the ring face and expose the dominance of π- vs. σ-type H-bonding in the hydrated complexes as found for the Me2S-aromatics. Our modeling will inform how Met/MetOn-aromatic motifs are determinants of redox-induced changes in proteins.

Alternating donor–acceptor indigo-cyclopentadithiophene copolymers: competition between excited state conformational relaxation, energy transfer and excited state proton transfer

In a copolymer with indigo and CPDT, fast ESPT and/or intrachain energy transfer are observed whereas conformational relaxation is absent.

Study of the Conformational Variety of the Oligosaccharide Substrates of Neuraminidases from Pathogens using Molecular Modeling

Analysis of the conformational variety of the oligosaccharide fragments of the human glycan receptors LSTa (α-D-Neu5Ac-(2-3)-β-D-Gal-(1-3)-β-D-GlcNAc-(1-3)-β-D-Gal(1-4)-D-Glc) and LSTc (α-D-Neu5Ac-(2-6)-β-D-Gal-(1-3)-β-D-GlcNAc-(1-3)-β-D-Gal(1-4)-D-Glc) in aqueous solution has been performed with the comprehensive use of molecular modeling and statistical data processing followed by determination of major and minor stabilized conformers and selection of relevant topologies. The sialic acid ring conformational free energy landscape for both pentasaccharides has been reconstructed and analyzed giving a specification of the most probable distorted ring conformations of the basic chair 1C4 structure. The obtained results are in a good agreement with experimental data generated by nuclear magnetic resonance spectroscopy and X-ray crystallography.

Role of conformational dynamics in the evolution of novel enzyme function.

The free energy landscape concept that describes enzymes as an ensemble of differently populated conformational sub-states in dynamic equilibrium is key for evaluating enzyme activity, enantioselectivity, and specificity. Mutations introduced in the enzyme sequence can alter the populations of the pre-existing conformational states, thus strongly modifying the enzyme ability to accommodate alternative substrates, revert its enantiopreferences, and even increase the activity for some residual promiscuous reactions. In this feature article, we present an overview of the current experimental and computational strategies to explore the conformational free energy landscape of enzymes. We provide a series of recent publications that highlight the key role of conformational dynamics for the enzyme evolution towards new functions and substrates, and provide some perspectives on how conformational dynamism should be considered in future computational enzyme design protocols.

Chemometric modeling of larvicidal activity of plant derived compounds against zika virus vector Aedes aegypti: application of ETA indices.

Dengue, zika and chikungunya have severe public health concerns in several countries. Human modification of the natural environment continues to create habitats in which mosquitoes, vectors of a wide variety of human and animal pathogens, thrive, which can bring about an enormous negative impact on public health if not controlled properly. Quantitative structure–activity relationship (QSAR) modeling has been applied in this work with the aim of exploring features contributing to promising larvicidal properties against the vector Aedes aegypti (Diptera: Culicidae). A dataset of 61 plant derived compounds reported in previous literature was used in this present study. A genetic algorithm (GA) was used for QSAR model development employing the “Double Cross Validation” (DCV) tool available at http://teqip.jdvu.ac.in/QSAR_Tools/. The DCV tool removes any bias in descriptor selection from a fixed composition of a training set and often provides an optimum solution in terms of predictivity. Simple topological descriptors, the “Extended Topochemical Atom” (ETA) indices developed by the present authors' group, were used for model development. These descriptors do not require pretreatment of molecular structures by conformational analysis or energy minimization before model development, thus saving computational time and resources. They also avoid ambiguities with respect to the existence of compounds in various conformational states leading to the loss of predictive capability in QSAR models. A number of models were generated from GA, and further, the descriptors appearing in the best model obtained from GA were subjected to partial least squares (PLS) regression to obtain the final robust model. The developed model was validated extensively using different validation metrics to check the reliability and predictivity of the model for enhancing confidence in QSAR predictions. Based on the insights obtained from the PLS model, we can conclude that the presence of hydrogen bond acceptor atoms, the presence of multiple bonds as well as sufficient lipophilicity and a limited polar surface area play crucial roles in regulating the activity of the compounds.

The Polymorphs of ROY: A Computational Study of Lattice Energies and Conformational Energy Differences

The remarkable structural diversity observed in polymorphs of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (commonly known as ROY) challenges computational attempts to predict or rationalize their relative stability. This modest study explores the applicability of CE-B3LYP model energy calculation of lattice energies (using experimental crystal structures), supplemented by a systematic approach to account for conformational energy differences. The CE-B3LYP model provides sensible estimates of absolute and relative lattice energies for the polymorphs, provided care is taken to achieve convergence in the summation of pairwise terms. Conformational energy differences based on density functional theory (DFT) energies are shown to be unreliable, but MP2 energies based on DFT-optimized structures show considerable promise.

Highly Diastereoselective Synthesis of 2-(1-N-Boc-aminoalkyl)thiazole-5-carboxylates by Reduction of tert-Butylsulfinyl Ketimines.

Positional isomers of naturally occurring peptide subunits were synthesized via highly diastereoselective reduction of tert-butylsulfinyl ketimines as a key reaction. While NaBH4 reduction of ketimines derived from 2-thiazolyl ketones afforded the (RS,R)-isomer with moderate diastereoselectivity, L-Selectride® reduction afforded the (RS,S)-isomer as the sole product. In contrast, ketimines derived from tert-butyl 2-thiazolyl ketone afforded the (RS,R)-isomer with low diastereoselectivity by both NaBH4 and L-Selectride® reduction. Stereochemistry of the reaction was discussed based on calculation of the conformational energies for ketimines.

Exploring the enantiorecognition mechanism of Cinchona alkaloid-based zwitterionic chiral stationary phases and the basic trans-paroxetine enantiomers.

The enantiomers of trans-paroxetine (the selectand) were separated on four chiral stationary phases incorporating either quinine [ZWIX(+), ZWIX(+A)] or quinidine [ZWIX(-), ZWIX(-A)] and (R,R)-aminocyclohexanesulfonic acid [in ZWIX(-), and ZWIX(+A)] or (S,S)-aminocyclohexanesulfonic acid [in ZWIX(+), and ZWIX(-A)] chiral selectors. The zwitterion nature of the phases is due to the presence of either (R,R)- or (S,S)-aminocyclohexanesulfonic acid in the selector structure bearing the quinuclidine moiety. ZWIX(+) and ZWIX(-) phases are available on the market with the commercial names CHIRALPAK ZWIX(+) and CHIRALPAK ZWIX(-), respectively. With the aim of rationalizing the enantiomer elution order with the above chiral stationary phases, a molecular dynamic protocol was applied and two energetic parameters were initially measured: selectand conformational energy and selectand interaction energy. In the search for other descriptors allowing a better fitting with the experimental evidences, in the present work we consider an energetic parameter, defined as the selector conformational energy, which resulted to be relevant in the explanation of the experimental elution order in most of the cases. Very importantly, the computational data produced by the present study strongly support the outstanding role of the conformational energy of the chiral selector as it interacts with the analytes.

Hydrogen-bonding behavior of various conformations of the HNO3…(CH3OH)2 ternary system.

Nine minima were found on the intermolecular potential energy surface for the ternary system HNO3(CH3OH)2 at the MP2/aug-cc-pVDZ level of theory. The cooperative effect, which is a measure of the hydrogen-bonding strength, was probed in these nine conformations of HNO3…(CH3OH)2. The results are discussed here in terms of structures, energetics, infrared vibrational frequencies, and topological parameters. The cooperative effect was observed to be an important contributor to the total interaction energies of the cyclic conformers of HNO3…(CH3OH)2, meaning that it cannot be neglected in simulations in which the pair-additive potential is applied. Graphical abstract The H-bonding behavior of various conformations of the HNO3(CH3OH)2 trimer was investigated.

Amber-Compatible Parametrization Procedure for Peptide-like Compounds: Application to 1,4- and 1,5-Substituted Triazole-Based Peptidomimetics.

Peptidomimetics are molecules of particular interest in the context of drug design and development. They are proteolytically and metabolically more stable than their natural peptide counterparts but still offer high specificity toward their biological targets. In recent years, 1,4- and 1,5-disubstituted 1,2,3-triazole-based peptidomimetics have emerged as promising lead compounds for the design of various inhibitory and tumor-targeting molecules as well as for the synthesis of peptide analogues. The growing popularity of triazole-based peptidomimetics and a constantly broadening range of their application generated a demand for elaborate theoretical investigations by classical molecular dynamics simulations and molecular docking. Despite this rising interest, accurate and coherent force field parameters for triazole-based peptidomimetics are still lacking. Here, we report the first complete set of parameters dedicated to this group of compounds, named TZLff. This parametrization is compatible with the latest version of the AMBER force field (ff14SB) and can be readily applied for the modeling of pure triazole-based peptidomimetics as well as natural peptide sequences containing one or more triazole-based modifications in their backbone. The parameters were optimized to reproduce HF/6-31G* electrostatic potentials as well as MP2/cc-pVTZ equilibrium Hessian matrices and conformational potential energy surfaces through the use of a genetic algorithm-based search and least-squares fitting. Following the standards of AMBER, we introduce residue building units, thus allowing the user to define any given sequence of triazole-based peptidomimetics. Validation of the parameter set against ab initio- and NMR-based reference systems shows that we obtain fairly accurate results, which properly capture the conformational features of triazole-based peptidomimetics. The successful and efficient parametrization strategy developed in this work is general enough to be applied in a straightforward manner for parametrization of other peptidomimetics and, potentially, any polymeric assemblies.