Complete Geometry Optimization Research Articles

The Co-N bond cleavage in the adenosyncobalamin cofactor in advance to glutamate mutase and methylmalonyl-CoA mutase processes

The in vivo experiments show that the adenosylcobalamin cofactor in glutamate mutase and methylmalonyl-CoA mutase processes lose its dimethylbenzimidazole axial ligand before starting the enzymatic processes. Complete active space self-consistent field geometry optimization of the vitamin B12 active forms plus substrates joint models have been performed. These joint models include the adenosylcobalamin cofactor, the carboxyl negative ion model of the studied processes’ active substrates, and the histidine molecule. Partial electronic density is transferred from the highest occupied substrate molecular orbitals to the lowest unoccupied antibonding molecular orbitals, which consist of corrin ring and dimethylbenzimidazole ligand common molecular orbitals during the multi-configurational self-consistent field molecular orbital mixing process. As a result, the Co-N axial bond is permanently elongated during the complete active space self-consistent field geometry optimization until its complete rupture and until the removal of the dimethylbenzimidazole ligand from the central cobalt atom and the corrin ring is complete. The Co-N bond cleavage in the adenosylcobalamin cofactors in the studied processes is running as no energy barrier process under the influence of their active substrates and histidine molecule.

Mechanochemical synthesis and structure of a nanocluster {organosilicon dendrimer - Copper dimer}

A novel nanocluster (organosilicon dendrimer - copper dimer) G1–8S-Dec•2CuCl2 was synthesized by a mechanochemical method. Optical and IR spectroscopy, NMR and ESR methods confirm that mechanochemical action on the mixture (dendrimer G1–8S-Dec + anhydrous copper (II) chloride) leads to the formation of a structure in which two copper atoms are linked by exchange interaction and are stabilized in the form of a dimer by sulfur atoms in the structure of the dendrimer G1–8S-Dec. A quantum mechanical calculation was carried out using the density differential method (DFT), which proved the possibility of the existence of two tetrahedral complexes SCuCl3 connected by a common face of chlorine atoms and having sulfur atoms at the vertices located in the branches of the dendrimer. The structure of the Cu2Cl4Si5C116H244S8 nanocluster is calculated by complete geometry optimization. It was found that the synthesized cluster implements the Dzyaloshinsky - Moriya interaction and exhibits multiferroic properties.

Phytoconstituents of Methanolic Extract of Fenugreek Seeds as a Green Corrosion Inhibitor of Metals (Fe, Al and Cu)

DFT calculations were carried out on significant Fenugreek seed compounds (1-Methylpyridinium-3-carboxylate MPC, Apigenin-8-C-glucose ACG, and 2-Isobutyl-3-methoxypyrazine IBMP) as a green source of ecologically friendly Fe, Al, and Cu metal corrosion inhibitors. Complete geometry optimizations were performed by DFT-B3LYP/6-31G* to determine any relationship between the chemical structure and corrosion inhibition, mostly on metals' surfaces. Global computational parameters of the inhibitors and thermodynamic Gibbs process of adsorption of metals were calculated and used to evaluate each corrosion inhibitor's performance. Our findings showed that MPC has the maximum anti-corrosion efficiency across all molecules with a physical adsorption mechanism. It exhibited significant inhibition efficiency with Cu when compared with Fe and Al, based on the highest electrophilicity index (ω) values compared to other inhibitors and its impact on metals in the following manner: Cu>Fe>Al. In regards, the range of inhibitors increased by the following order: IBMP>ACG>MPC. Remarkable corrosion inhibition of MPC is demonstrated by its unique high electrophilicity, softness (σ), and lowest ∆Egap on the metal surface. These outcomes are close to the experimental

Molecular spectroscopic assembly of 3-(4-chlorophenyl)-5-[4-(propane-2-yl) phenyl] 4, 5-dihydro-1H pyrazole-1-carbothioamide, antimicrobial potential and molecular docking analysis

A novel pyrazole derivative 3-(4-Chlorophenyl)-5-[4-(propane-2-yl) phenyl] 4, 5-dihydro-1H –pyrazole-1-carbothioamide (CPDPC) was optimized to its minimum energy level using density functional theory (DFT) method. The complete optimization of the molecular equilibrium geometry of the title molecule was carried out. Quantum chemical calculations of the equilibrium geometry and the complete vibrational assignments of wavenumber using potential energy distribution (PED) were carried out using DFT method (B3LYP) with 6–311++G (d, p) basis set. Frontier molecular orbitals such as highest molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and molecular electrostatic potential surface on the title molecule are predicted for various intramolecular interactions that are responsible for the stabilization of the molecule. Stability of the molecule arising from hyper conjugative interactions, charge delocalization and intramolecular hydrogen bond-like weak interaction has been analyzed using 6–311++G (d,p) basis set. From the UV–Visible spectrum, the electronic properties such as excitation energies, oscillator strength and wavelength are calculated by DFT method. The title compound has been screened for their in vitro antimicrobial activity against four bacteria and two fungal strains using disc diffusion and broth microdilution susceptibility assays. From the molecular docking studies, it is evident that the Cl atom attached to phenyl ring and carbothioamide group attached to pyrazole ring is crucial for binding and the result draws us to the conclusion that the compound might exhibit antimicrobial activity.

Synthesis, Conformational Analysis, Infrared, Raman and UV-Visible Spectra of Novel Schiff Bases compiled with DFT Calculations.

Two novel Schiff bases named, 2-((2-Hydroxybenzylidene)amino)-4,5,6,7- tetrahydrobenzo[b] thiophene-3-carbonitrile (BESB1) and 2-((Furan-2-ylmethylene)amino)-4,5,6, 7-tetrahydro-benzo[b]thiophene-3-carbonitrile (BESB2) were synthesized. The structures were characterized based on CHN elemental analysis, mid-infrared (400- 4000 cm-1), Raman (100-4000 cm-1), 1H NMR, mass and UV-Vis spectroscopic measurements. In addition, quantum mechanical calculations using DFT-B3LYP method at 6-31G(d) basis set were carried out for both Schiff bases. Initially, we have carried out complete geometry optimizations followed by frequency calculations for the proposed conformational isomers; BESB1 (A-E) and BESB2 (F-J) based on the orientations of both CN and OH groups against the azomethine lonepair (NLP) in addition to the 3D assumption. The computational outcomes favor conformer A for BESB1 in which the C≡N and OH moieties are cis towards the NLP while conformer G is preferred for BESB2 (the C≡N/furan-O are cis/trans towards the NLP) which was found consistent with the results of relaxed potential energy surface scan. Aided by normal coordinate analysis of the Cartesian coordinate displacements, we have suggested reliable vibrational assignments for all observed IR and Raman bands. Moreover, the electronic absorption spectra for the favored conformers were predicted in DMSO solution using TD-B3LYP/6-31G(d) calculations. Similarly, the 1H NMR chemical shifts were also estimated using GIAO approach implementing PCM including solvent effects (DMSO-d6). Proper interpretations of the observed electronic transition, chemical shifts, IR and Raman bands were presented in this study.

Molecular docking, spectroscopic studies on 4-[2-(Dipropylamino) ethyl]-1,3-dihydro-2H-indol-2-one and QSAR study of a group of dopamine agonists by density functional method.

Density functional theory is one of the most popular accepted computational quantum mechanical techniques used in the analysis of molecular structure and vibrational spectra. Experimental and theoretical investigations of the molecular structure, electronic and vibrational characteristics of 4-[2-(Dipropylamino) ethyl]-1,3-dihydro-2H-indol-2-one are presented in this work. The title compound was characterized using FT-IR, FT-Raman and UV-Vis spectroscopic techniques. The results were compared with the theoretical calculations obtained using DFT/B3LYP with 6-311++G(d,p) as basis sets and was found to be in good agreement. The complete optimization of the molecular geometry of the title compound was carried out. Further, the vibrational assignments and calculation of potential energy distribution (PED) were reported. NLO has emerged as a key factor in recent researches. Materials showing nonlinear optical properties form the basis of nonlinear optics and development of such materials plays an important role in the present scenario. The current work provides sufficient justification for the title compound to be selected as a good non-linear optical (NLO) candidate. The electronic properties were reported using TD-DFT approach. The HOMO (EHOMO = -5.96 eV), LUMO (ELUMO = -0.80 eV) energies, energy gap and electrophilicity (2.22) was calculated in order to understand the stability, reactivity and bioactivity of the compound under investigation. To comprehend the bonding interactions we have performed the total (TDOS), partial (PDOS) and overlap population or COOP (Crystal Orbital Overlap Population) density of states. The drug likeness values were analyzed to evaluate the potential of the title compound to be an active pharmaceutical component. As a positive proof the paper further explains the molecular docking studies of the said compound. In addition, the stereochemistry of the protein structure was checked using Ramachandran plot. The title compound is a directly acting dopamine D2 agonist. In order to establish relationship between molecular descriptors of compound and its biological activity, QSAR studies have been done within the framework of DFT for 10 dopamine agonist including the title compound. Hence, the research exploration provides requisite information pertaining to the geometry, stability, reactivity and bioactivity of the compound through spectroscopic and quantum chemical methods.

Quantitative structure-activity relationship and molecular docking studies of some series of imidazole derivatives as anti-hepatitis C drug

Hepatitis C virus (HCV) NS5B RNA-depended-RNA-polymerase (RdRp) is an essential enzyme in HCV viral replication and has no functional equivalent in mammalian cells. In silico study was carried out to develop a Quantitative structure activity-relationship and molecular docking on some selected imidazole derivatives as anti-hepatitis C compounds. Density functional theory with B3LYP/6-311G* was employed for complete geometry optimization Five QSAR models were generated using Genetic Function Algorithm (GFA) of the material studio software version 8, in which model one (1) was selected as the best model and reported based on the validation parameter with the squared correlation coefficient (R 2 ) of 0.7114. Adjusted squared correlation coefficient (R 2 adj) value 0f 0.6458 and cross-validation coefficient (Q 2 ) LOO 0.5810. The best model that is model (1) was subjected to external validation and was found to be R 2 pred. = 0.5729. The result obtained from molecular docking studies shows that the compound with the best binding affinity of -10.7 Kcal/mol formed hydrogen bonding of (GLN 446 and GLU143) and hydrophobic interaction with the amino acid residues of the Non-Structural 5B polymerase(NS5B polymerase) receptor. The QSAR model and molecular docking results propose the direction of designing new imidazole derivatives agent with better activity against the NS5B polymerase target site. Keywords: Binding affinity, HCV, imidazole, molecular docking, NS5B polymerase, QSAR

Computational studies of some biscoumarin and biscoumarin thiourea derivatives as alfa-glucosidase inhibitors

Quantitative structure-activity relationship and molecular docking studies of 35 compounds of Biscoumarins and Biscoumarins thiourea derivatives as alfa-glucosidase inhibitors was performed. Density Functional Theory (DFT) method was employed for complete geometry optimization of the alfa-glucosidase inhibitors. Genetic Function Algorithm (GFA) of the material studio was utilized to develop four models. Model 1 was found to be the best model with R2 = 0.914362, R2 adj = 0.892953, Q2cv = 0.858197 and R2 pred = 0.614745. The proposed model is robustness and predicted with good internal and external validation. The descriptors should be considered when improving the inhibitory activities of biscoumarin derivatives against alfa-glucosidase. The docking results showed that ligands having Ortho substituted phenyl ring have good interactions with active site residues and good inhibitory activities as compared to ligands having either Para or Meta substituted phenyl ring except ligand 16 which has the highest docking scores of -12.5 kcal/mol but undergoes para substitution on the phenyl ring and formed hydrogen bond, hydrophobic and electrostatic interactions with the active residues of the enzyme. The QSAR model and molecular docking results agree with each other and give way to the designing of new inhibitors with better activity against alfa-glucosidase.

Spectroscopic (FT-IR, FT Raman) and quantum mechanical study on N-(2,6-dimethylphenyl)-2-{4-[2-hydroxy-3-(2-methoxyphenoxy)propyl]piperazin-1-yl}acetamide

Density Functional Theory (DFT) approach has become one of the most cost effective means to investigate upon the molecular structure and vibrational spectrum and are finding widespread use in the applications related to biological systems. Investigations (experimental and theoretical) on the molecular structure, electronic and vibrational characteristics of N-(2,6-dimethylphenyl)-2-{4-[2-hydroxy-3-(2-methoxyphenoxy)propyl]piperazin-1-yl}acetamide are reported in this work. DFT/B3LYP method was used to obtain the vibrational frequencies using 6-311++G (d,p) basis set. On comparison, experimental FT-IR and FT-Raman spectral data were in good agreement with the results obtained from computational methods. The complete optimization of the molecular equilibrium geometry of the title compound was carried out. Quantum chemical calculations of the equilibrium geometry and the complete vibrational assignments of wavenumbers using potential energy distribution (PED) were carried out. HOMO-LUMO energy gap was found to be 4.75eV. The stability and charge delocalization of the title molecule were studied by Natural Bond Orbital (NBO) analysis. Non Linear Optical (NLO) behavior in terms of first order hyperpolarizability and dipole moment which was found to be 1.3 × 10−30 e.s.u and 2.36D respectively. Molecular Electrostatic Potential (MEP) was mapped. Thermodynamic properties of the title molecule were studied and the correlations with temperatures were analyzed. Molecular Docking studies were carried out for the title compound.

Fourier transform infrared and Raman spectroscopy in the study of phase transitions in dipyrazolium iodide triiodide: Experimental and theoretical analysis

The paper presents the Infrared and Raman spectra of the powdered [C3N2H5+]2[I−∙I3−] crystal at the temperature intervals of 11–270K, covering two low-temperature phase transitions: discontinuous at 182/188K (cooling/heating) and continuous at 254K. The research shows that the vibrational states of the pyrazolium cations change significantly during discontinuous phase transition (III→II), while the continuous nature of successive structural transformation is more subtle and displays an insignificant change in the temperature coefficient of numerous vibrations during the II→I PT at 254K. The spectacular changes at Raman spectra above 188K confirm a huge rebuilding of inorganic network from [I−∙I3−] to [I42−]. Additionally, a complete geometry optimization was carried out in the solid state in order to obtain minimum structures and bonding properties. The theoretical results correspond well with the experimental data. Moreover, the infrared spectrum in harmonic approximation was calculated, and a comparative vibrational analysis was performed. CRYSTAL09 vibrational results appear to be in a good agreement with the experimental ones.

Evaluation of corrosion protection of epoxy coatings on copper during exposure to an aerated 3% NaCl solution.

In this study the anticorrosion performance of a clear epoxy coating was enhanced by the incorporation of modified zinc into the polymer matrix. The structural macroscopy by X-ray diffraction (XRD). Corrosion performance of the coated copper specimens was investigated employing polarization measurements and electrochemical impedance spectroscopy (EIS) in 3% NaCl solution. Incorporation of 5 wt% zinc possessed the best corrosion performance. The electrochemical results are completely in agreement with the morphological results of the surface obtained from scanning electron microscopy (SEM). For the theoretical study, complete geometry optimization of 4, 4′- Ethylene bis (N, N diglycidylaniline) was performed using the Density Functional Theory (DFT). The Gaussian 03W software package was used in the calculations.

Molecular design of new π-conjugated materials based on pyrimidine for organic solar cellsapplication

The research in new π-conjugated molecules with specific applications has become one of the most interesting topics in the fields of chemical physics and materials science.In fact, these compounds have been widely explored, thanks to their essential particular properties, as novel class of promising materials in the field of optoelectronics. In this work, we emphasize the importance of the materials based on pyrimidine π- conjugated derivatives due to their strong potential for solar cell applications. The Density Functional Theory (DFT) approach at B3LYP level and 6-31G(d,p) orbital basis sets for all atoms as implemented in Gaussian 09 program has been used for complete geometry optimization with no constraints of pyrimidine π-conjugated based derivatives.The assessed molecular properties comprise the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), and other molecular properties derived from HOMO and LUMO and their respective energies. The absorption spectra were simulated by Time-Dependent Density Functional Theory (TD/DFT) at the B3LYP/6-31G(d,p) level owing to the calculation of the oscillator strengths, the maximum absorption wavelengths and the excitation energy corresponding to the pyrimidine π-conjugated derivatives. The open circuit voltage and the difference between both the LUMO energy levels of the donor and the acceptor have been also evaluated. Hence, we have scanned the rapport, for the molecules under study, between the molecular, the electronic structure and the efficiency of the solar cell in order to give further insights on the possibility of electron transfer between the donor and the acceptor entities. Our results lead to the likelihood to suggest pyrimidine based materials as bulkheterojunction solar cell for organic solar cells application.

Quantitative structure-toxicity relationships and molecular highlights about Aedes aegypti larvicidal activity of monoterpenes and related compounds

Dengue is a viral tropical disease transmitted to humans via the bite of Aedes aegypti L. (Diptera: Culicidae) mosquitoes. Since there is no specific treatment for dengue, the only method for preventing virus transmission is to control its vector by using environmental management and chemical methods. In this work, we propose a quantitative structure-toxicity relationships study of 31 monoterpenes and structurally related compounds which are bioactive against Aedes aegypti larvae, aiming to identify structural features responsible for the compounds activity, with the goal to support lead optimization. After conformational studies and complete geometry optimizations in DFT level, 1666 descriptors were calculated by E-Dragon online platform. The ordered predictors selection algorithm selected nine important descriptors, which were reduced to three after further analysis (R8e+, MAXDN, nCt), considering twenty-four and seven compounds in training and test sets, respectively. The validation parameters of final MLR modeling for these variables were: R2 = 0.83; Q2loo = 0.77; Q2ext = 0.83, showing that a robust and predictive model was obtained.

A Theoretical Study of the Enol Contents of Cyclohexanone, Cyclopentanone and Acetone

PM3 and DFT calculations have been performed with complete optimization of geometries on cyclohexanone, cyclopentanone, and acetone. The enol content trend determined in this work was cyclohexanone > cyclopentanone > acetone, which was found to agree with published experimental and theoretical works. Equilibrium constants, strain energies of enols, and electron distributions are reported.

Density Functional Theory Investigations on the Geometric and Electronic Structures of 4–Azidomethyl–6–Isopropyl–2H–Chromen–2–One

We have employed first principle Density Functional Theory (DFT) investigations to study the physical and electronic properties of 4-Azidomethyl-6-isopropyl-2H-chromen-2-one, C13H13N3O2. Complete geometry optimization calculations were carried out to find local energy minimum of the molecular system using the B3LYP approach with a variety of basis sets. The optimized geometries were then used to determine the HOMO-LUMO gaps, Mulliken atomic charges, and others. Our calculation results show that the computed geometrical properties of C13H13N3O2 cluster model are in good agreement with the corresponding measured experimental value. The calculated energies obtained are close to each other using the B3LYP density functional method combined with a variety of basis sets. Furthermore, using B3LYP/6-31G** method, the oxygen-attached carbon, C2 atom has the highest positively charge, with the corresponding value of +0.59. For both oxygen atoms (O1 and O2), the calculated charge values obtained are about -0.52 and -0.46, respectively.

Evaluating the accuracy of density functional theory for calculating 1H and 13C NMR chemical shifts in drug molecules

The accuracy of different DFT methodologies for calculating 1H and 13C NMR chemical shifts in (R)-ispinesib, a complex drug molecule with multiple chemical groups and one stereocentre, has been evaluated. The accuracy of 6 basis sets and 16 different XC functionals was tested. In addition, we present a detailed study on the role of geometry optimisation (in gas and solution phase using a chloroform polarisable continuum model) on the accuracy of the calculated NMR spectra. NMR calculations using the double-ζ basis sets DGDZVP and 6-31++G(d,p) were found to be more accurate (and computationally more efficient) than those using larger triple-ζ basis sets. The O3LYP/DGDZVP methodology in solution phase using a geometry optimised at the same level of theory was found to be the most accurate method with mean absolute errors (MAEs) for 1H and 13C chemical shifts of 0.174ppm and 3.972ppm, respectively. Irrespective of the choice of XC or basis set used, complete geometry optimisation in either gas or solvent phase was found to be essential for attaining the highest accuracy in both 1H and 13C calculated chemical shifts. Finally, the role of molecular conformation was examined by calculating the Boltzmann-weighted 1H and 13C chemical shifts. Overall, we demonstrate that DFT shows exceptional promise for use in calculating the NMR chemical shifts in complex drug molecules. In the future, DFT calculations of NMR parameters are set to play an increasingly important role in drug discovery and chemical optimisation.

Structural and Electronic Properties of Poly(9,9-dialkylfluorene)-Based Alternating Copolymers in Solution: An NMR Spectroscopy and Density Functional Theory Study

The structural and electronic properties of three alternating poly(9,9-dialkylfluorene) copolymers, poly[2,7-(9,9-bis(octyl)-fluorene)-alt-benzothiadiazole] (F8BT), poly[2,7-(9,9-bis(2′-ethylhexyl)-fluorene)-alt-thiophene S,S-dioxide] (PFTSO2), and poly[2,7-(9,9-bis(2′-ethylhexyl)-fluorene)-alt-1,4-phenylene] (PFP), containing, respectively, benzothiadiazole (BT), thiophene S,S-dioxide, and phenylene groups, have been investigated and compared to those of the homopolymer poly[2,7-(9,9-bis(2′-ethylhexyl)-fluorene)] (PF2/6). The NMR spectra and corresponding shielding tensors of the 1H and 13C nuclei have been studied in solution and are interpreted by density functional theory (DFT) with complete geometry optimization using the B3LYP functional. Particular emphasis is placed on the conformational behavior and electronic properties in the electronic ground state. In addition, time-dependent DFT is applied to obtain detailed insight into the character of selected excited states. A new TDDFT interpretation is presented for optical absorption spectra of singlet and triplet states that have previously been reported for these fluorene-based conjugated copolymers using photoexcitation and pulse radiolysis-energy transfer studies. As well as providing detailed assignment of excited states, the results show that the triplet excitation is slightly more localized than S1 excitation, in agreement with experimental observations. The DFT analysis provides a link between structure and NMR, optical, electronic properties, allowing optimization of the potential of such polymers for photovoltaic and electroluminescence applications.

Ab-initio study of the ground state structure and properties of Fe+2 (thymine)2 (H2O)2 complex

Hartree-Fock calculations with 6-31G (d) basis set have been done in the gas phase on Fe+2 (thymine)2 (H2O)2 complex with complete geometry optimization. Stable structure for the complex has been found. Single point water phase calculation (PCM) has also been done which shows that the complex is more stable in water implying its physiological action for the removal of excess hazardous Fe+2 from the body. Selected optimized geometrical parameters, charge densities on selected atoms have been reported. HOMO-LUMO energies and structures are shown. The LUMO structure shows that the Fe+2 play the key role of the complex. The study may help in the new drug discovery. Key words: Gaussian, gas phase, water phase, Hartree-Fock, charge density.

Quantum chemical simulation of silicon tetrachloride hydrogenation

The quantum chemical calculation of the activation parameters of the reduction of a SiCl4 molecule with molecular hydrogen, atomic hydrogen, and atomic chlorine was performed. The energy parameters were determined within the scope of the density functional theory (DFT) with the complete geometry optimization by the unrestricted UB3LYP/6-311+G(d) method. The calculated activation energies allow one to exclude the participation of molecular hydrogen in processes of dehalogenation of chlorosilanes.

Conformational Preferences of Modified Nucleoside N2-methylguanosine (m2G) and Its Derivative N2, N2-dimethylguanosine (m 2 2 G) Occur at 26th Position (Hinge Region) in tRNA

Conformational preferences of the modified nucleosides N(2)-methylguanosine (m(2)G) and N(2), N(2)-dimethylguanosine (m(2)(2)G) have been studied theoretically by using quantum chemical perturbative configuration interaction with localized orbitals (PCILO) method. Automated complete geometry optimization using semiempirical quantum chemical RM1, along with ab initio molecular orbital Hartree-Fock (HF-SCF), and density functional theory (DFT) calculations has also been made to compare the salient features. Single-point energy calculation studies have been made on various models of m(2)G26:C/A/U44 and m(2)(2)G26:C/A/U44. The glycosyl torsion angle prefers "syn" (χ = 286°) conformation for m(2)G and m(2)(2)G molecules. These conformations are stabilized by N(3)-HC2' and N(3)-HC3' by replacing weak interaction between O5'-HC(8). The N(2)-methyl substituent of (m(2)G26) prefers "proximal" or s-trans conformation. It may also prefer "distal" or s-cis conformation that allows base pairing with A/U44 instead of C at the hinge region. Thus, N(2)-methyl group of m(2)G may have energetically two stable s-trans m(2)G:C/A/U or s-cis m(2)G:A/U rotamers. This could be because of free rotations around C-N bond. Similarly, N(2), N(2)-dimethyl substituent of (m(2)(2)G) prefers "distal" conformation that may allow base pairing with A/U instead of C at 44th position. Such orientations of m(2)G and m(2)(2)G could play an important role in base-stacking interactions at the hinge region of tRNA during protein biosynthesis process.