Theoretical ab initio study of the effects of methylation on structure and stability of G:C Watson-Crick base pair

Methylation of DNA occurs most readily at N(3), N(7), and O(6) of purine bases and N(3) and O(2) of pyrimidines. Methylated bases are continuously formed through endogenous and exogenous mechanisms. The results of a theoretical ab initio study on the methylation of G:C base pair components are reported. The geometries of the local minima were optimized without symmetry restrictions by the gradient procedure at DFT level of theory and were verified by energy second derivative calculations. The standard 6-31G(d) basis set was used. The single-point calculations have been performed at the MP2/6-31G(d,p), MP2/6-31++G(d,p), and MP2/6-311++G(2d,2p) levels of theory. The geometrical parameters, relative stability and counterpoise corrected interaction energies are reported. Also, using a variation-perturbation energy decomposition scheme we have found the vital contributions to the total interaction energy.     

DFT studies on the intrinsic conformational properties of non-ionic pyrrolysine in gas phase

B3LYP/6-31G(d,p) level of theory is used to carry out a detailed gas phase conformational analysis of non-ionized (neutral) pyrrolysine molecule about its nine internal back-bone torsional angles. A total of 13 minima are detected from potential energy surface exploration corresponding to the nine internal back-bone torsional angles. These minima are then subjected to full geometry optimization and vibrational frequency calculations at B3LYP/6-31++G(d,p) level. Characteristic intramolecular hydrogen bonds present in each conformer, their relative energies, theoretically predicted vibrational spectra, rotational constants and dipole moments are systematically reported. Single point calculations are carried out at B3LYP/6-311++G(d,p) and MP2/6-31++G(d,p) levels. Six types of intramolecular H-bonds, viz. O…H–O, N…H-O, O…H–N, N…H–N, O…H–C and N…H–C, are found to exist in the pyrrolysine conformers; all of which contribute to the stability of the conformers. The vibrational frequencies are found to shift invariably toward the lower side of frequency scale corresponding to the presence of intramolecular H-bond interactions in the conformers.     

Ab Initio Quantum Mechanics Analysis of Imidazole C-H…O Water Hydrogen Bonding and a Molecular Mechanics Forcefield Correction

Abstract

While it is well established that classical hydrogen bonds play an important role in enzyme structure, function and dynamics, the role of weaker, but ‘activated’ C-H donor hydrogen bonds is poorly understood. The most important such case involves histidine which often plays a direct role in enzyme catalysis and possesses the most acidic C-H donor group of the standard amino acids. In the present study, we obtained optimized geometries and hydrogen bond interaction energies for C-H…O hydrogen bonded complexes between methane, ethylene, benzene, acetylene, and imidazole with water at the MP2-FC/6-31++G(2d,2p) and MP2-FC/aug-cc-pVDZ//MP2-FC/6-31++G(2d,2p) levels of theory. A strong linear relationship is obtained between the stability of the various hydrogen bonded complexes and both separation distances for H…0 and C—O. In general, these calculations indicate that C-H…0 interactions can be classified as hydrogen bonding interactions, albeit significantly weaker than the classical hydrogen bonds, but significantly stronger than just van der Waals interactions. For instance, while the electronic energy of stabilization at the MP2-FC/aug-cc-pVDZ//MP2-FC/6-31++G(2d,2p) level of theory of a water C-H…O water hydrogen bond is 4.36 kcal/mol more stable than the methane C-H…O water interaction, the water-water hydrogen bond is only 2.06 kcal/mol more stable than the imidazole C_e?H…O water hydrogen bond. Neglecting this latter hydrogen bonding interaction is obviously unacceptable. We next compare the potential energy surfaces for the imidazole C_e?H…O water and imidazole N_d?H…O hydrogen bonded complexes computed at the MP2/6-31++G(2d,2p) level of theory with the potential energy surface computed using the AMBER molecular mechanics program and forcefields. While the Weiner et al and Cornell et al AMBER forcefields reasonably account for the imidazole N-H…O water interaction, these forcefields do not adequately account for the imidazole C_e?H…O water hydrogen bond. A forcefield modification is offered that results in excellent agreement between the ab initio and molecular mechanics geometry and energy for this C-H…O hydrogen bonded complex.     

A Theoretical Study of the cis-syn Pyrimidine Dimers in the Gas Phase and Water Cluster and a Tautomer-Bypass Mechanism for the Origin of UV-induced Mutations

Abstract

A quantum mechanical study of all cis-syn cyclobutane pyrimidine photodimers including the normal and rare tautomeric forms of bases has been performed using the ab initio method at HF/6–31G(d,p), MP2(fc)//HF/6–31G(d,p) and MP2(fc)/6–31G(d,p) levels. A puckering angle of the cyclobutyl ring and twist angle of pyrimidine rings with respect to each other is well described by these calculations. It is predicted that in the gas phase all photodimers containing the rare imino form of cytosine are more stable than those containing its normal form. The Monte Carlo simulations show that the dimer containing the imino form of cytosine is more stabilized by water cluster than that containing its amino forms. The possible biological significance stems from the fact that the cytosine in the dimer directs the incorporation of adenine in the complementary strand during replicative bypass. Data obtained point to the cytosine tautomerism as a possible mechanism for the origin of UV-induced mutation.     

An assessment to evaluate the validity of different methods for the description of some corrosion inhibitors

New research and development efforts using computational chemistry in studying an assessment of the validity of different quantum chemical methods to describe the molecular and electronic structures of some corrosion inhibitors were introduced. The standard and the highly accurate CCSD method with 6-311++G(d,p), ab initio calculations using the HF/6-31G++(d,p) and MP2 with 6-311G(d,p), 6-31++G(d,p), and 6-311++G(2df,p) methods as well as DFT method at the B3LYP, BP86, B3LYP*, M06L, and M062x/6-31G++(d,p) basis set level were performed on some triazole derivatives and sulfur containing compounds used as corrosion inhibitors. Quantum chemical parameters, such as the energy of the highest occupied molecular orbital energy (E_HOMO), the energy of the lowest unoccupied molecular orbital energy (E_LUMO), energy gap (ΔE), dipole moment (μ), sum of total negative charges (TNC), chemical potential (Pi), electronegativity (χ), hardness (η), softness (σ), local softness (s), Fukui functions (f ⁺,f ^?), electrophilicity (ω), the total energy change (?E_T) and the solvation energy (S.E), were calculated. Furthermore, the accuracy and the applicability of these methods were estimated relative to the highest accuracy and standard CCSD with 6-311++G(d,p) method. Good correlations between the quantum chemical parameters and the corresponding inhibition efficiency (IE%) were found.     

Theoretical Ab initio study of the effects of methylation on the nature of hydrogen bonding in A:T base pair

We report the results of a theoretical ab initio study of methylation in Watson-Crick A:T base pairs. Equilibrium geometries were obtained without symmetry restrictions by the gradient procedure at DFT level of theory with the standard 6-31G(d) basis set. Each local minima was verified by energy second derivative calculations. Single-point calculations for the DFT geometries have been performed at the MP2/6-31G(d,p), MP2/6-31++G(d,p), and MP2/6-311++G(2d,2p) levels of theory. The geometrical parameters, relative stabilities and counterpoise corrected interaction energies are reported. In addition, using a variation-perturbation energy decomposition scheme, we have found the important contributions to the total interaction energy.     

Theoretical study of geometrical and nonlinear optical properties of pyridinum N-phenolate betaine dyes

This paper presents an ab initio quantum chemical investigation of the geometrical structures and the non-linear optical properties (NLO) of three structural isomers of pyridinium N-phenolate betaine dye. The ground state geometrical parameters and the first-order hyperpolarizabilities were calculated using the Hartree-Fock (HF) as well as the second-order perturbation Møller-Pleset (MP2) method with the 6–31G, 6–31G(d), 6–31G(d,p), 6–31+G(d), 6–31++G(d,p), 6–311+G(d), aug-cc-PVDZ and the recently developed Z3PolX basis sets. Moreover, the first-order hyperpolarizability was calculated at the coupled cluster singles and doubles (CCSD/6–31+G(d)) level of theory. The analysis of the results of calculations for the investigated isomers indicates that there are important differences in their NLO activities. Additionally, it was shown that Z3PolX basis set works reasonable well for betaine dyes.

Theoretical investigation on the structure and thermodynamic properties of the 2,4-dinitroimidazole complex with methanol

The structure and thermodynamic properties of the 2, 4-dinitroimidazole complex with methanol were investigated using the B3LYP and MP2(full) methods with the 6-31++G(2d,p) and 6-311++G(3df,2p) basis sets. Four types of hydrogen bonds [N–H?O, C–H?O, O–H?O (nitro oxygen) and O–H?π] were found. The hydrogen-bonded complex having the highest binding energy had a N–H?O hydrogen bond. Analyses of natural bond orbital (NBO) and atoms-in-molecules (AIM) revealed the nature of the intermolecular hydrogen-binding interaction. The changes in thermodynamic properties from monomers to complexes with temperatures ranging from 200.0 to 800.0 K were investigated using the statistical thermodynamic method. Hydrogen-bonded complexes of 2,4-dinitroimidazole with methanol are fostered by low temperatures.

Quantum-chemical investigation of tautomerization ways of Watson-Crick DNA base pair guanine-cytosine

A novel physico-chemical mechanism of the Watson-Crick DNA base pair Gua.Cyt tautomerization Gua.Cyt*<---->Gua.Cyt<---->Gua*.Cyt (mutagenic tautomers of bases are marked by asterisks) have been revealed and realized in a pathway of single proton transfer through two mutual isoenergetic transition states with Gibbs free energy of activation 30.4 and 30.6 kcal/mol and they are ion pairs stabilized by three (N2H...N3, N1H...N4- and O6+H...N4-) and five (N2H...O2, N1H...O2, N1H...N3, O6+H...N4- and 06+H...N4-) H-bonds accordingly. Stable base pairs Gua-Cyt* and Gua*.Cyt which dissociate comparably easy into monomers have acceptable relative Gibbs energies--12.9 and 14.3 kcal/mol--for the explanation of the nature of the spontaneous transitions of DNA replication. Results are obtained at the MP2/6-311++G(2df,pd)//B3LYP/6-31 1++G(d,p) level of theory in vacuum approach.     

Theoretical investigation of the gas-phase reactions of CF2ClC(O)OCH3 with the hydroxyl radical and the chlorine atom at 298 K

A Theoretical study on the mechanism of the reactions of CF₂ClC(O)OCH₃ with the OH radical and Cl atom is presented. Geometry optimization and frequency calculations have been performed at the MPWB1K/6-31+G(d,p) level of theory and energetic information is further refined by calculating the energy of the species using G2(MP2) theory. Transition states are searched on the potential energy surface involved during the reaction channels and each of the transition states are characterized by presence of only one imaginary frequency. The existence of transition states on the corresponding potential energy surface is ascertained by performing intrinsic reaction coordinate (IRC) calculation. Theoretically calculated rate constants at 298 K and atmospheric pressure using the canonical transition state theory (CTST) are found to be in good agreement with the experimentally measured ones. Using group-balanced isodesmic reactions as working chemical reactions, the standard enthalpies of formation for CF₂ClC(O)OCH_3, CF₂ClC(O)OCH₂ and CF₃C(O)OCH₃ are also reported for the first time.     

Is 1-nitro-1-triazene a high energy density material?

An azo bridge (–N?=?N–) can not only desensitize explosives but also dramatically increase their heats of formation and explosive properties. Amino and nitro are two important high energy density functional groups. Here, we present calculations on 1-nitro-1-triazene (NH₂–N?=?N–NO₂). Thermal stability and detonation parameters were predicted theoretically at CCSD(T)/6-311G* level, based on the geometries optimized at MP2/6-311G* level. It was found that the p?→?π conjugation interaction and the intramolecular hydrogen bonding that exist in the system together increase the thermal stability of the molecule. Moreover, the detonation parameters were evaluated to be better than those of the famous HMX and RDX. Finally, the compound was demonstrated to be a high energy density material.     

A theoretical study of cooperative and anticooperative effects on hydrogen-bonded clusters of water and the cyanuric acid

Ab initio and density functional calculations are used to analyse the interaction between a molecule of the cyanuric acid and one, two and three molecules of water at B3LYP/6-311++ G(d,p) and MP2/6-311++ G(d,p) computational levels. Also, the cooperative effect (CE) in terms of the stabilisation energy of clusters is calculated and discussed. Depending on the geometry of clusters under study, the cooperative, non- or anti-CE was found with an increasing cluster size. Red shifts of N–H and C = O stretching frequencies illustrate a good dependence on the CE. The atoms in molecules theory is used to analyse the CE on topological parameters.     

Theoretical study of the reaction mechanism of CH<Subscript>3</Subscript>NO<Subscript>2</Subscript> with NO<Subscript>2</Subscript>, NO and CO: the bimolecular reactions that cannot be ignored

The intriguing decompositions of nitro-containing explosives have been attracting interest. While theoretical investigations have long been concentrated mainly on unimolecular decompositions, bimolecular reactions have received little theoretical attention. In this paper, we investigate theoretically the bimolecular reactions between nitromethane (CH₃NO₂)—the simplest nitro-containing explosive—and its decomposition products, such as NO₂, NO and CO, that are abundant during the decomposition process of CH₃NO₂. The structures and potential energy surface (PES) were explored at B3LYP/6-31G(d), B3P86/6-31G(d) and MP2/6-311?+?G(d,p) levels, and energies were refined using CCSD(T)/cc-pVTZ methods. Quantum chemistry calculations revealed that the title reactions possess small barriers that can be comparable to, or smaller than, that of the initial decomposition reactions of CH₃NO₂. Considering that their reactants are abundant in the decomposition process of CH₃NO₂, we consider bimolecular reactions also to be of great importance, and worthy of further investigation. Moreover, our calculations show that NO₂ can be oxidized by CH₃NO₂ to NO₃ radical, which confirms the conclusion reached formerly by Irikura and Johnson [(2006) J Phys Chem A 110:13974–13978] that NO₃ radical can be formed during the decomposition of nitramine explosives.     

MP2, density functional theory, and molecular mechanical calculations of C-H···π and hydrogen bond interactions in a cellulose-binding module-cellulose model system

Exploring non-covalent interactions, such as C-H···π stacking and classical hydrogen bonding (H-bonding), between carbohydrates and carbohydrate-binding modules (CBMs) is an important task in glycobiology. The present study focuses on intermolecular interactions, such as C-H?π (sugar-aromatic stacking) and H-bonds, between methyl β-d-glucopyranoside and l-tyrosine—a proxy model system for a cellulose-CBM complex. This work has made use of various types of quantum mechanics (QM) and molecular mechanics (MM) methods to determine which is the most accurate and computationally efficient. The calculated interaction potential energies ranged between −24 and −38 kJ/mol. The larger interaction energy is due to H-bonding between the phenyl hydroxyl of tyrosine and the O4 of the sugar. Density functional theory (DFT) methods, such as BHandHLYP and B3LYP, exaggerate the H-bond. Although one of the MM methods (viz. MM+) considered in this study does maintain the C-H?π stacking configuration, it underestimates the interaction energy due to the loss of the H-bond. When the O-H bond vector is in the vicinity of O4 (O-H?O4 ≈ 2 Å, e.g., in the case of MP2/6-31G(d)), the torsional energy drops to a minimum. For this configuration, natural bond orbital (NBO) analysis also supports the presence of this H-bond which arises due to orbital interaction between one lone pair of the sugar O4 and the σ∗(O-H) orbital of the phenyl group of tyrosine. The stabilization energy due to orbital delocalization of the H-bonded system is ∼13 kJ/mol. This H-bond interaction plays an important role in controlling the CH/π interaction geometry. Therefore, the C-H?π dispersive interaction is the secondary force, which supports the stabilization of the complex. The meta-hybrid DFT method, M05-2X, with the 6-311++G(d,p) basis set agrees well with the MP2 results and is less computationally expensive. However, the M05-2X method is strongly basis set dependent in describing this CH/π interaction. Computed IR spectra with the MP2/6-31G(d) method show blue shifts for C1-H, C3-H, and C5-H stretching frequencies due to the C-H?π interaction. However, the M05-2X/6-311++G(d,p) method shows a small red shift for the C1-H stretching region and blue shifts for the C2-H and C3-H stretches. For the aromatic tyrosine C_δ1-C_ε1 and C_δ2-C_ε2 bonds in the complex, the calculated IR spectra show red shifts of 12 cm⁻¹ (MP2/6-31G(d)) and 5 cm⁻¹ (M05-2X/6-311++G(d,p)). This study also reports the upfield shifts of computed ¹H NMR chemical shifts due to the C-H?π interaction.     

The reaction of the aminoboranylidene-iminoborane isomerization: a CASSCF direct dynamics study

The barrier and the potential-energy surface of the isomerization from aminoboranylidene (BNH₂) to iminoborane (HBNH) have been studied using complete active space self-consistent field (CASSCF) with the 6−31+G(d, p) basis set and higher-level energy methods. The rate constants of the isomerization reaction are reported by employing the direct ab initio dynamics method. The geometries of all the stationary points were optimized using the B3LYP and CCSD methods with the cc-pVTZ and cc-pVQZ basis sets. The information along the intrinsic reaction coordinate (IRC) was also calculated at the CASSCF/6−31+G (d,p) level of theory. The energies were refined at the G3, G3MP2, G3MP2B3, CBS-Q, CBS-QB3, and two high-level (HL) methods based on the geometries optimized using CASSCF/6-31+G(d,p). The rate constants were evaluated using conventional transition-state theory (TST), canonical variational transition-state theory (CVT), and canonical variational transition-state theory with small curvature tunneling correction (CVT/SCT) and conventional transition-state theory with Eckart tunneling correction (TST/Eckart). According to the calculated results, we conclude that the tunneling effect is very important to this isomerization reaction.     

Correlated ab initio molecular dynamics simulations of the acetone–carbon dioxide complex: implications for solubility in supercritical CO2

Ab initio molecular dynamics simulations of the acetone–CO₂ complex (MP2/6-31G(d) level) were performed to investigate the effect of dynamics at finite temperature on the weak electron donor–acceptor intermolecular interactions. In addition, we carried out a study of the free energy of formation of the complex by means of umbrella sampling technique at the MP2 level with a perturbative CCSD(T) correction. The potential of mean force was obtained along a reaction coordinate describing the acetone–CO₂ interaction. The results obtained here support some hypothesis that we already explored in past works using static electronic calculations. In particular, when interacting with a molecule having a carbonyl function, carbon dioxide displays both Lewis acid and Lewis base behaviour. This property can be exploited to design molecular systems that are easily solubilised in supercritical CO₂.     

Structural and vibrational spectroscopic elucidation of sulpiride in solid state

The study on the conformational and vibrational behaviors of sulpiride molecule which is known as a neuroleptic or antipsychotic drug that is widely used clinically in the treatment of schizophrenic or depressive disorders is an important scientific and practical task. In here, a careful enough study of monomer and dimeric forms of sulpiridine {5-(aminosulfonyl)-N-[(1-ethyl-2-pyrrolidinyl) ethyl]-2-methoxy-benzamide (C₁₅H₂₃N₃O₄S)} is undertaken by density functional theory (DFTB3LYP) method with the B3LYP/6-31G(d,p) basis set. The conformations of free molecule were searched by means of torsion potential energy surfaces scan studies through dihedral angles D₁ (8?N, 18C, 20C, 23?N), D₂ (18C, 20C, 23?N, 25C) and D₃ (28C, 30C, 41S, 44?N) in electronically ground state, employing 6-31G basic set. The final geometrical parameters for the obtained stable conformers were determined by means of geometry optimization, carried out at DFT/B3LYP/6-31G(d,p) theory level. Afterwards, the possible dimer forms of the molecule were formed and their energetically preferred conformations were investigated. Moreover, the effect of basis set superposition error on the structure and energy of the three energetically favourable sulpiride dimers has been determined. The optimized structural parameters of the most stable monomer and three low energy dimer forms were used in the vibrational wavenumber calculations. Raman and IR (4000–400?cm^?1) spectra of sulpiride have been recorded in the solid state. The assignment of the bands was performed based on the potential energy distribution data. The natural bond orbital analysis has been performed on both monomer and dimer geometries in order to elucidate delocalization of electron density within the molecule. The predicted frontier molecular orbital energies at DFT/B3LYP/6-31G(d,p) theory level show that charge transfer occurs within the molecule. The first-order hyperpolarizability (β₀) and related properties (μ and α) of the title molecule were also calculated.     

A theoretical study of the cis-syn pyrimidine dimers in the gas phase and water cluster and a tautomer-bypass mechanism for the origin of UV-induced mutations

A quantum mechanical study of all cis-syn cyclobutane pyrimidine photodimers including the normal and rare tautomeric forms of bases has been performed using the ab initio method at HF/6-31G(d.p), MP2(fc)//HF/6-31G(d,p) and MP2(fc)/6-31G(d,p) levels. A puckering angle of the cyclobutyl ring and twist angle of pyrimidine rings with respect to each other is well described by these calculations. It is predicted that in the gas phase all photodimers containing the rare imino form of cytosine are more stable than those containing its normal form. The Monte Carlo simulations show that the dimer containing the imino form of cytosine is more stabilized by water cluster than that containing its amino forms. The possible biological significance stems from the fact that the cytosine in the dimer directs the incorporation of adenine in the complementary strand during replicative bypass. Data obtained point to the cytosine tautomerism as a possible mechanism for the origin of UV-induced mutation.     

Comparative theoretical study of the UV/Vis absorption spectra of styrylpyridine compounds using TD-DFT calculations

This study examined absorption properties of 2-styrylpyridine, trans-2-(m-cyanostyryl)pyridine, trans-2-[3-methyl-(m-cyanostyryl)]pyridine, and trans-4-(m-cyanostyryl)pyridine compounds based on theoretical UV/Vis spectra, with comparisons between time-dependent density functional theory (TD-DFT) using B3LYP, PBE0, and LC-ωPBE functionals. Basis sets 6–31G(d), 6–31G(d,p), 6–31+G(d,p), and 6–311+G(d,p) were tested to compare molecular orbital energy values, gap energies, and maxima absorption wavelengths. UV/Vis spectra were calculated from fully optimized geometry in B3LYP/6–311+G(d,p) in gas phase and using the IEFPCM model. B3LYP/6–311+G(d,p) provided the most stable form, a planar structure with parameters close to 2-styrylpyridine X-ray data. Isomeric structures were evaluated by full geometry optimization using the same theory level. Similar energetic values were found: ～4.5 kJ?mol^?1 for 2-styrylpyridine and ～1 kJ?mol^?1 for derivative compound isomers. The 2-styrylpyridine isomeric structure differed at the pyridine group N-atom position; structures considered for the other compounds had the cyano group attached to the phenyl ring m-position equivalent. The energy difference was almost negligible between m-cyano-substituted molecules, but high energy barriers existed for cyano-substituted phenyl ring torsion. TD-DFT appeared to be robust and accurate approach. The B3LYP functional with the 6–31G(d) basis set produced the most reliable λ_max values, with mean errors of 0.5 and 12 nm respect to experimental values, in gas and solution, respectively. The present data describes effects on the λ_max changes in the UV/Vis absorption spectra of the electron acceptor cyano substituent on the phenyl ring, the electron donor methyl substituent, and the N-atom position on the electron acceptor pyridine ring, causing slight changes respect to the 2-styrylpyridine title compound.