Isoenergetic Conformers Research Articles

Молекулярное моделирование конформационной подвижности молекулы гиламбатина

The features of the spatial organization of the hylambatin molecule were investigated by methods of molecular mechanics and molecular dynamics. Hylambatin consists of twelve amino acid residues in the sequence: Asp-Pro-Pro-Asp-Pro-Asn-Arg-Phe-Tyr-Gly-Met-Met-NH2. Unlike all other tachykinins, hylambatin has a Met residue replacing the usual Leu at penultimate position. The tachykinin peptide hylambatin has been isolated and chemically characterized from methanol extracts of the skin of Hylambates maculatus, an African rhacophorid frog. It has been shown that intravenously administered hylambatin significantly increases the level of glucose and insulin in blood plasma. In this paper, the conformational flexibility of the hylambatin molecule was studied by methods of molecular mechanics and molecular dynamics. The conformational calculation of the peptide took into account non-valent and electrostatic interactions, hydrogen bonds and torsion potentials. Based on fragmentary analysis, stable spatial structures of the hylambatin dodecapeptide were determined, which can be represented as a set of conformations characterized by a relatively labile N-terminal tetrapeptide and a conformationally rigid C-terminal octapeptide. In the calculated stable conformational states, the effective interactions of the side chains of residues and hydrogen bonds were refined and energetically evaluated. It has been shown that the hylambatin molecule preferably forms practically isoenergetic conformations with various structural types at the N-end of the peptide chain, passing into the alpha helix at the C-end. By the method of molecular dynamics, the pattern of intramolecular mobility of stable conformations of the hylambatin molecule was modeled both in vacuum and surrounded by water molecules. Based on the calculated values of the dihedral angles, molecular models of energetically preferred conformational states of the hylambatin dodecapeptide were constructed.

Inter-enantiomer conversion dynamics and Johari\u2013Goldstein relaxation of benzophenones

We employ temperature- and pressure-dependent dielectric spectroscopy, as well as differential scanning calorimetry, to characterize benzophenone and the singly-substituted ortho-bromobenzophenone derivative in the liquid and glass states, and analyze the results in terms of the molecular conformations reported for these molecules. Despite the significantly higher mass of the brominated derivative, its dynamic and calorimetric glass transition temperatures are only ten degrees higher than those of benzophenone. The kinetic fragility index of the halogenated molecule is lower than that of the parent compound, and is found to decrease with increasing pressure. By a detailed analysis of the dielectric loss spectra, we provide evidence for the existence of a Johari–Goldstein (JG) relaxation in both compounds, thus settling the controversy concerning the possible lack of a JG process in benzophenone and confirming the universality of this dielectric loss feature in molecular glass-formers. Both compounds also display an intramolecular relaxation, whose characteristic timescale appears to be correlated with that of the cooperative structural relaxation associated with the glass transition. The limited molecular flexibility of ortho-bromobenzophenone allows identifying the intramolecular relaxation as the inter-enantiomeric conversion between two isoenergetic conformers of opposite chirality, which only differ in the sign of the angle between the brominated aryl ring and the coplanar phenyl-ketone subunit. The observation by dielectric spectroscopy of a similar relaxation also in liquid benzophenone indicates that the inter-enantiomer conversion between the two isoenergetic helicoidal ground-state conformers of opposite chirality occurs via a transition state characterized by a coplanar phenyl-ketone moiety.

The Formation of C3O3H6 Structural Isomers in the Gas Phase through Barrierless Pathways: Formation and Spectroscopic Characterization of Methoxy Acetic Acid

Abstract Gas phase formation processes feasible at low temperatures are determined theoretically for 38 isomers obeying the C3O3H6 empirical formula, one of them, the simplest ketose dihydroxyacetone, has been observed in gas phase sources. A preliminary search for isomeric forms first targets ethoxy formic acid (C2H5–O–COOH) as the most stable isomer followed by lactic acid. Profiles corresponding to the minimum energy pathways reveal that the favored conformers of 14 of these isomers can be formed in the gas phase through 29 barrierless processes involving the OH*, CH3O*, HCO*, CH3*, CH2OH, HCOO*, and OHCO* radicals, all of them observed in the interstellar medium. Kinetic rates are provided at 200, 298, and 500 K, confirming the suitability of 16 processes at low temperatures. Faster processes involve the OH hydroxyl radical whereas, to a lesser degree, the processes involving the HOCO radical and the methoxy methyl radical CH3O*, are quite significant. Spectroscopic parameters (rovibrational and torsional) are obtained for methoxy acetic acid (CH3–O–CH2COOH) for which two low-lying isoenergetic conformers can be produced from the CH3OCH2* radical predicted to be a precursor of abundant observed molecules. Profiles and spectroscopic properties make methoxy acetic acid a good candidate to be detected in the gas phase of extraterrestrial sources.

Microwave spectrum and structure of the SO3−SO2 weakly bound complex

The microwave spectrum and structure of the weakly bound complex SO3–SO2 are reported. The parent species, as well as the isotopologues with 34S and 33S single substitution on each sulfur atom have been observed. Together with the measured 33S nuclear quadrupole coupling constants, the structure of the complex has been determined. MP2/6-311++G(3df) calculations identify two nearly isoenergetic conformations, one of which corresponds to the observed structure. In the observed complex, an oxygen atom of the SO2 approaches the sulfur of the SO3 with an intermolecular S⋯O distance of 2.635(28) Å. The experimental S⋯S distance is 3.7517(83) Å, and the SO2 is positioned so as to direct an oxygen lone electron pair roughly along the C3 axis of the SO3. This structure reflects the strong acidity of SO3 insofar as it is suggestive of incipient electron pair donation from the SO2 oxygen to the acidic site of the SO3.

Interplay between Conformation and Crystal Packing in Aryl Propargyl Ethers: Structural and Spectroscopic Properties of 2‐(prop‐2‐yn‐1‐yloxy)acene Derivatives

AbstractThe 2‐(prop‐2‐yn‐1‐yloxy)naphthalene (compound I) and 1‐nitro‐2‐(prop‐2‐yn‐1‐yloxy)benzene (compound II) were prepared in excellent yields by the reaction of propargyl bromide with 2‐naphthol and 2‐nitrophenol, respectively. Structural and conformational properties of both compounds have been analyzed using a combined approach including single‐crystal X‐ray diffraction and quantum chemical calculations. Two forms are found to be stable and nearly isoenergetic conformers, depending on the mutual orientation of the C≡C triple bond and the O–C single bond of the prop‐2‐yn‐1‐yloxy group. The gauche conformation is the most stable form for the vacuum isolated species, with the anti conformation higher in energy by 1.00 and 1.89 kcal/mol computed at the M06‐2X/6‐311++G(d,p) level of approximation, for I and II, respectively. The gauche form is observed in the crystal of I but the nearly planar anti conformation is adopted in the crystalline phase of compound II. The occurrence of C–H⋅⋅⋅π and C–H⋅⋅⋅O intermolecular interactions involving the acidic ‐C≡C–H hydrogen donor and ‐C≡C‐ and ‐OCH2– acceptors is discussed. Furthermore, vibrational features of the prop‐2‐yn‐1‐yloxy moiety are analyzed by infrared and Raman spectroscopy. The UV‐Vis spectrum shows the presence of well‐defined absorption at ca. 280 and 320 nm assigned to the π→π* transitions in the naphtyl/benzyl and prop‐2‐yn‐1‐yloxy groups, respectively.

Dynamic Conformational Behavior in Stable Pentaorganosilicates

Silicates with five organic groups are conformationally dynamic even with two bidentate ligands. Symmetry breaking by incorporating a single nitrogen or phosphorus atom provides insight into their dynamic behavior. N‐containing silicates with bidentate 2‐phenylpyridine, biphenyl, and a Me (8), Et (9) or Ph (10) ligand were studied comprehensively by NMR spectroscopy and DFT theory to reveal two isoenergetic conformers with a barrier of ca. 10 kcal mol–1. P‐containing silicate 14 with bidentate triphenylphosphane, biphenyl, and Me ligands is subject to multiple Berry pseudorotations, turnstile rotations, and conformational flexibility of the P‐center. The stability increased by masking the P‐center with a BH3 group (16). DFT and NMR modeling reveal two isoenergetic conformers for 16 with a barrier of ca. 19 kcal‧mol–1 for a complex interconversion pathway. This barrier bodes well for the design of configurationally stable chiral‐at‐metal transition metal catalysts.

QFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.

Proteins and ligands sample a conformational ensemble that governs molecular recognition, activity, and dissociation. In structure-based drug design, access to this conformational ensemble is critical to understand the balance between entropy and enthalpy in lead optimization. However, ligand conformational heterogeneity is currently severely underreported in crystal structures in the Protein Data Bank, owing in part to a lack of automated and unbiased procedures to model an ensemble of protein-ligand states into X-ray data. Here, we designed a computational method, qFit-ligand, to automatically resolve conformationally averaged ligand heterogeneity in crystal structures, and applied it to a large set of protein receptor-ligand complexes. In an analysis of the cancer related BRD4 domain, we found that up to 29% of protein crystal structures bound with drug-like molecules present evidence of unmodeled, averaged, relatively isoenergetic conformations in ligand-receptor interactions. In many retrospective cases, these alternate conformations were adventitiously exploited to guide compound design, resulting in improved potency or selectivity. Combining qFit-ligand with high-throughput screening or multitemperature crystallography could therefore augment the structure-based drug design toolbox.

Duplication of a Single Strand in a β-Sheet Can Produce a New Switching Function in a Photosensory Protein.

Duplication of a single β-strand that forms part of a β-sheet in photoactive yellow protein (PYP) was found to produce two approximately isoenergetic protein conformations, in which either the first or the second copy of the duplicated β-strand participates in the β-sheet. Whereas one conformation (big-loop) is more stable at equilibrium in the dark, the other conformation (long-tail) is populated after recovery from blue light irradiation. By appending a recognition motif (E-helix) to the C-terminus of the protein, we show that β-strand duplication, and the resulting possibility of β-strand slippage, can lead to a new switchable protein-protein interaction. We suggest that β-strand duplication may be a general means of introducing two-state switching activity into protein structures.

Conformational flexibility and base-pairing tendency of the tobacco carcinogen O6-[4-oxo-4-(3-pyridyl)butyl]guanine

The present work uses DFT calculations to characterize the conformational and hydrogen-bonding properties of O6-[4-oxo-4-(3-pyridyl)butyl]guanine (POB-G), a DNA adduct caused by tobacco. POB-G is found to adopt many isoenergetic conformations that allow for discrete interactions between the bulky moiety and the adducted G and/or pairing base. The calculated structure and stability of the hydrogen-bonded pairs between the Watson-Crick or Hoogsteen face of POB-G and the canonical DNA nucleobases fully rationalize the previously reported mutational spectra. Specifically, the stable, non-distorted pseudo-Watson-Crick POB-G:T pair explains the predominant G➔A mutations, while the stable, yet marginally distorted pairs between the Watson-Crick face of POB-G and A or C clarify the G➔T mutations and non-mutagenic replication. Finally, the stable, yet highly distorted Hoogsteen POB-G:G pair rationalizes the experimentally-observed insertion but lack of persistence of G opposite POB-G in DNA. Overall, these structural insights are critical for guiding future studies that strive to fully understand the adduct mutagenicity, including the accessible conformations and the replication of POB-G-adducted DNA.

Conformation of protonated glutamic acid at room and cryogenic temperatures.

Recognition properties of biologically relevant molecules depend on their conformation. Herein, the conformation of protonated glutamic acid (H+Glu) isolated in quadruple ion traps is characterized by vibrational spectroscopy at room and cryogenic temperatures and dispersion-corrected density functional theory calculations at the B3LYP-D3/aug-cc-pVTZ level. The infrared multiple photon dissociation (IRMPD) spectrum recorded in the fingerprint range at room temperature using an IR free electron laser is attributed to the two most stable and nearly isoenergetic conformations (1-cc and 2-cc) with roughly equal population (ΔG298 = 0.0 kJ mol-1). Both have bridging C[double bond, length as m-dash]O(HNH)+O[double bond, length as m-dash]C ionic H-bonds of rather different strengths but cannot be distinguished by their similar IRMPD spectra. In contrast, the higher-resolution single-photon IRPD spectrum of H2-tagged H+Glu recorded in the conformation-sensitive X-H stretch range in a trap held at 10 K distinguishes both conformers. At low temperature, 1-cc is roughly twice more abundant than 2-cc, in line with its slightly lower calculated energy (ΔE0 = 0.5 kJ mol-1). This example illustrates the importance of cryogenic cooling, single-photon absorption conditions, and the consideration of the X-H stretch range for the identification of biomolecular conformations involving hydrogen bonds.

Conformational Exploration of Enflurane in Solution and in a Biological Environment.

Enflurane is a fluorinated volatile anesthetic, whose bioactive conformation is not known. Actually, a few studies have reported on the conformations of enflurane in nonpolar solution and gas phase. The present computational and spectroscopic (infrared and NMR) work shows that three pairs of isoenergetic conformers take place in the gas phase, neat liquid, polar, and nonpolar solutions. According to docking studies, a single conformation is largely preferred over its isoenergetic isomers to complex with the active site of Integrin LFA-1 enzyme (PDB code: 3F78 ), where the widely used anesthetic isoflurane (a constitutional isomer of enflurane) is known to bind. Weak hydrogen bonding from an electrostatic interaction between the CHF2 hydrogen and the central CF2 fluorines was not found to rule the conformational isomerism of enflurane. Moreover, intramolecular interactions based on steric, electrostatic, and hyperconjugative effects usually invoked to describe the anomeric effect are not responsible for the possible bioactive conformation of enflurane, which is rather governed by the enzyme induced fit.

The conformation of enkephalin bound to its receptor: an “elusive goal” becoming reality

The availability of solid state structures of opioid receptors has prompted us to reconsider a crucial question concerning bioactive peptides: can their conformation be studied without any knowledge of the structure of their receptors? The possibility of giving a meaningful answer to this query rests ultimately on the ease of dealing with the flexibility of bioactive peptides, and amongst them one of the most flexible bioactive peptides, enkephalin. All solution studies of enkephalin hint at an inextricable mixture of quasi isoenergetic conformers. In this study we refer to the only NMR work that yielded inter-residue NOEs, performed at very low temperature. In the present work, we have used the simplest possible docking methods to check the consistency of the main conformers of enkephalin with the steric requirements of the active site of the receptor, as provided by the crystal structure of its complex with naltrindole, a rigid antagonist. We show that the conformers found in the equilibrium mixture at low temperature are indeed compatible with a good fit to the receptor active site. The possible uncertainties linked to the different behavior of agonists and antagonists do not diminish the relevance of the finding.

Crystal structure, matrix-isolation FTIR, and UV-induced conformational isomerization of 3-quinolinecarboxaldehyde.

The crystal structure of 3-quinolinecarboxaldehyde (3QC) has been solved, and the compound has been shown to crystallize in the space group P21/c (monoclinic) with a = 6.306(4), b = 18.551(11), c = 6.999(4) Å, β = 106.111(13)°, and Z = 4. The crystals were found to exhibit pseudomerohedral twinning with a twin law corresponding to a two-fold rotation around the monoclinic (100) reciprocal lattice axis (or [4 0 1] in direct space). Individual molecules adopt the syn conformation in the crystal, with the oxygen atom of the aldehyde substituent directed toward the same side of the ring nitrogen atom. In the gas phase, the compound exists in two nearly isoenergetic conformers (syn and anti), which could be successfully trapped in solid argon at 10 K, and their infrared spectra are registered and interpreted. Upon in situ irradiation of matrix-isolated 3QC with UV light (λ > 315 nm), significant reduction of the population of the less stable anti conformer was observed, while that of the conformational ground state (syn conformer) increased, indicating occurrence of the anti → syn isomerization. Upon irradiation at higher energy (λ > 235 nm), the syn → anti reverse photoreaction was observed. Interpretation of the structural, spectroscopic, and photochemical experimental data received support from quantum chemical theoretical results obtained at both DFT/B3LYP (including TD-DFT investigation of excited states) and MP2 levels, using the 6-311++G(d,p) basis set.

Absolute configuration of 1,5-diazepin-2-ones: A critical test case for density functional theory

The absolute configuration of a series of 4(R)-methyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-ones is assigned by comparison of experimental and calculated CD spectra using time-dependent density functional theory (TDDFT) in combination with four different functionals (B3PW91, CAM-B3LYP, M06-2X, BMK). Closest agreement with experiment is obtained with B3PW91. All compounds except those bearing an acyl group at N5 exist in two nearly isoenergetic conformations of the seven-membered ring (G⩽0.5kcalmol−1 with the local pair natural orbital coupled-electron pair approximation LPNO-CEPA/1/def2-TZVPP//B3LYP/6-311G(d,p)). Agreement between simulated and experimental CD spectra was found to critically depend on a proper description of conformer population as well as the position of the calculated longest-wavelength transitions of the individual conformers.

Methylparaben Isolated in Solid Argon: Structural Characterization and UV-Induced Conversion into Methylparaben Radical and Isomeric Ketenes

Methylparaben (methyl p-hydroxybenzoic acid; MP) is a widely used antimicrobial preservative, being the most frequently used antimicrobial preservative in cosmetics. The generalized use of MP has become controversial, with several recent reports of dangerous side effects. For example, the presence of MP in human breast tumors and its harmful effects on human skin exposed to the sunlight have been demonstrated. In spite of the important practical relevance of the compound and of the controversy about its practical use, its structural and photochemical characterization had not been undertaken hitherto. To fill this gap, in the present study, MP was isolated in solid argon (T = 15 K) and structurally characterized by a combined infrared spectroscopy/quantum chemistry approach. The potential energy surface (PES) of the molecule was investigated in detail, revealing the existence of two almost isoenergetic (ΔE(0) = 0.37 kJ mol(-1)) s-cis carboxylic ester low-energy conformers, with an estimated population ratio in the gas phase at room temperature (∼298 K) of ca. 0.83. The calculations also predicted the existence of two high-energy (ΔE(0) = ∼50 kJ mol(-1)) s-trans carboxylic ester conformers of MP. Upon isolation of the compound in an argon matrix, only the lowest energy conformer was found to survive, due to occurrence of extensive conformational cooling during matrix deposition. The infrared spectrum of this conformer was obtained and interpreted. In addition, the chemical processes resulting from in situ irradiation of the matrix-isolated MP with a broadband UV source (λ > 234 nm) were investigated, revealing extensive conversion of MP into highly reactive methylparaben radical and isomeric ketenes. These observations support the recent concerns regarding uses of MP, in particular when the compound has to be exposed to UV light.

Mass Spectrometry Study and Infrared Spectroscopy of the Complex Between Camphor and the Two Enantiomers of Protonated Alanine: The Role of Higher‐Energy Conformers in the Enantioselectivity of the Dissociation Rate Constants

The properties of the protonated complexes built from S camphor and R or S alanine were studied in a Paul ion trap at room temperature by collision-induced dissociation (CID) and infrared multiple-photon dissociation spectroscopy (IRMPD), as well as molecular dynamics and ab initio calculations. While the two diastereomer complexes display very similar vibrational spectra in the fingerprint region, in line with similar structures, and almost identical calculated binding energies, their collision-induced dissociation rates are different. Comparison of the IRMPD results to computed spectra shows that the SS and SR complexes both contain protonated alanine strongly hydrogen-bonded to the keto group of camphor. The floppiness of this structure around the NH⁺...O=C hydrogen bond results in a complex potential energy surface showing multiple minima. Calculating the dissociation rate constant within the frame of the transition state theory shows that the fragmentation rate larger for the heterochiral SR complex than the homochiral SS complex can be explained in terms of two almost isoenergetic low-energy conformers in the latter that are not present for the former.

MD SIMULATION STUDIES TO INVESTIGATE ISO-ENERGETIC CONFORMATIONAL BEHAVIOUR OF MODIFIED NUCLEOSIDES M2G AND M22G PRESENT IN tRNA

Modified nucleic acid bases are most commonly found in tRNA. These may contain modifications from simple methylation to addition of bulky groups. Methylation of the four canonical nucleotide bases at a wide variety of positions is particularly prominent among the known modification. Methylation of N2 group of guanine is a relatively common modification in tRNA and rRNA. N2-methylguanosine (m2G) is the second most often encountered nucleoside in E. coli tRNAs. N2, N2-dimethylguanosine (m22G) is found in the majority of eukaryotic tRNAs and involved in forming base pair interactions with adjacent bases. Hence, in order to understand the structural significance of these methylated nucleic acid bases we have carried out molecular dynamics simulation to see the salvation effect. The results obtained shows iso-energetic conformational behaviors for m2G and m22G. The simulation trajectory of m2G shows regular periodical fluctuations suggesting that m2G is equally stable as either s-cis or s-trans rotamers. The two rotamers of m2G may interact canonically or non-canonically with opposite base as s-trans m2G26:C/A/U44 and s-cis m2G26:A/U44. The free rotations around the C-N bond could be the possible reason for these iso-energetic conformations. Dimethylation of G has almost no influence on base pairing with either A or U. Thus, these results reveal that modified nucleosides m2G and m22G may play an important role to prevent tRNA from adopting the unusual mitochondrial like conformation.

Multidimensional OH local mode calculations for OH−(H2O)3—Importance of intermode anharmonicity

We present theoretical calculations on the vibrational spectra between the energy range of 2000-4000 cm(-1) for 4 isoenergetic conformers of gas phase OH(-)(H(2)O)(3) and OH(-)(H(2)O)(3)·Ar clusters. The peak positions and associated intensities of the OH stretching vibrations were calculated using an extended local mode model on multi-dimensional ab initio potential energy surfaces and dipole moment functions obtained by MP2/6-311++G(3df,3pd). Furthermore, to simulate the experimental spectra directly, both the homogeneous and inhomogeneous line widths were determined theoretically. For the ionic hydrogen bonded OHs, which directly bind to the OH(-), anharmonic coupling between the OHs on different water units is crucial for the reproduction of experimentally observed features. On the other hand, the coupling between free OH stretching vibrations is so small that the usual 1-dimensional local mode model provides a good and economical way to obtain the spectra. By comparing the theoretical spectra for 4 isoenergetic conformers, we found that the ionic hydrogen bonded OH stretching peaks can act as a descriptor for the subtle conformational differences in the first solvation shell. Furthermore, we showed that the coupling between the ionic hydrogen bonded OH and low frequency OO stretching vibrations can cause fairly strong combination bands, and that the weakly bound argon, which was used as a messenger in the experiment by Robertson et al. [Science; 2003, 299, 1367], causes shifts on the peak positions for the ionic hydrogen bonded OHs. In addition, we quantified the effect of counterpoise correction on the simulated spectra for the ionic hydrogen bonded OHs.

Rational Design of a Nonbasic Molecular Receptor for Selective NH4+/K+ Complexation in the Gas Phase

A new molecular receptor (1) for ammonium recognition has been designed and constructed by using only carbon atoms. This molecular receptor can co-exist in two different isoenergetic conformations but, upon complexation, the conformers are no longer isoenergetic, and a basket-shaped conformation becomes clearly more stable. The pre-organised tetrahedral structure of this basket-shaped molecule favours the complexation of ammonium ions by N-H⋅⋅⋅π interactions with the four phenyl groups of the host. A similar behaviour is not observed in a similar, but less pre-organised, reference molecule. ESI-MS competition experiments show that 1 is able to bind NH(4)(+) over K(+) selectively. This is the first example of a neutral molecular receptor that shows a remarkable NH(4)(+)/K(+) selectivity. DFT-calculations provide insight into the nature of host-guest interactions of both 1⋅NH(4)(+) and 1⋅K(+) complexes as well as in the mechanism involved in multiple cation-π interactions and the influence of these interactions on the conformational stability and the selective binding of the host.

Structural significance of hypermodified nucleic acid base hydroxywybutine (OHyW) which occur at 37th position in the anticodon loop of yeast tRNAPhe

Conformational preferences of hypermodified nucleic acid base hydroxywybutine (OHyW) have been studied using quantum chemical single point semi-empirical PM3 method. Automated geometry optimization using semi-empirical RM1, molecular mechanics force field (MMFF) along with ab-initio HF-SCF (6-31G** basis set) and DFT (B3LYP/6-31G** basis set) calculations have also been made to compare the salient features. Molecular electrostatic potentials (MEPs) depict the polarities of hydroxywybutine (OHyW) side chain. Another conformational study showed that hydroxywybutosine side chain interacts with adjacent bases within the anticodon loop of tRNAPhe. The solvent accessible surface area (SASA) calculations revealed the structural role of hydroxywybutine in anticodon loop. Explicit molecular dynamics (MD) simulation has been done over the PM3 most stable structure of OHyW. The hydroxywybutine side chain prefers ‘distal’ conformation i.e. spreads away from the cyclic five membered imidazole moiety of modified tricyclic guanine base. The predicted preferred conformation of hydroxywybutine may prevent extended Watson–Crick base pairing during protein biosynthesis process. This conformation of OHyW stabilized by intramolecular interactions between O(6)⋯HO(16), O(6)⋯HC(15) and O(20)⋯HC(17). Further stabilization is also expected from interactions between O(22)⋯HC(16) and O(23)⋯HC(15). Explicit molecular dynamics (MD) simulation over the PM3 most stable structure of OHyW support the preferred geometry by preserving the ‘distal’ orientation of hydroxywybutine side chain and intramolecular hydrogen bonding interactions. MD simulation study revealed the role of hydroxyl group of OHyW to avoid fluctuations and prevent multiple iso-energetic conformations of hydroxywybutine side chain as compared to wybutine (yW).