Energy Curves For Rotation Research Articles

Adsorption of cytarabine and gemcitabine anticancer drugs on the BNNT surface: DFT and GD3-DFT approaches

In this work, at first, in order to find the most stable conformers of the two types of anticancer cytarabine (CYT) and gemcitabine (GEM) drugs, the potential energy curves for rotation around the C1′-N bond were explored at M06-2X/6–311 + + G(2d,2p) level of theory. Adsorption of the most stable conformers of CYT and GEM drugs on the BNNT surface was explored. Depending on the orientation of CYT and GEM drugs on the outside surface of the BNNT, two different types of drug-BNNT adsorption complexes (A and B) were found on the potential energy surface. Dispersion corrected adsorption energies at M06-2X/6–31 + G(d)-GD3 level were in the range − 19.7 to − 26.1 kcal mol−1 for A1–A4 and − 21.7 to − 24.6 kcal mol−1 for B1–B4. The results show that adsorptions of CYT and GEM drugs on the BNNT surface in the water solvent are energetically favorable process. The structural and electronic density properties, charge transfer values, global reactivity descriptors and the molecular electrostatic potential maps of the drug-BNNT complexes were evaluated. It is anticipated that the complex formation accompanied by charge transfer between BNNT and drugs and the decrease in the HOMO − LUMO energy gap. The NCI (non-covalent interaction) analysis shows the role and importance of the cooperative π − π stacking and H-bonding interactions on the adsorption of drugs on the BNNT surface.

π Interactions Studied with Electronic Structure Methods: The Ethyne Methyl Isocyanide Complex and Thioanisole.

Two molecular systems for which previous studies had found qualitative differences in the results from calculations with the B3LYP and MP2 methods are investigated with a range of different electronic structure methods, including meta and double hybrid density functionals and DFT-D (DFT augmented with an empirical dispersion term). The performance of the different methods is assessed by comparison to estimated CCSD(T)/CBS (complete basis set) results. The first molecular system studied is the ethyne methyl isocyanide complex (CH3NC-C2H2), which exhibits π hydrogen bonds involving the C≡C and N≡C triple bonds. Earlier work on this system had shown that B3LYP predicts significantly longer hydrogen-bond distances than MP2. Here, we show that this is likely due to missing dispersion in the B3LYP calculations. On the basis of the CCSD(T) results, the ethyne methyl isocyanide interaction energy is estimated to be 12 ± 1 kJ/mol. B3LYP significantly underestimates the stability of the complex, whereas MP2 slightly overestimates. M05-2X, B3LYP-D, and (CP-corrected) mPW2-PLYP-D give results in close proximity to the CCSD(T) reference values. The second molecule investigated is thioanisole (C6H6SCH3), which can adopt two different conformations (thiomethyl group either planar or perpendicular with respect to the benzene ring). Potential energy curves for rotation around the C(sp(2))-S bond are computed and compared to the estimated CCSD(T)/CBS curve. CCSD(T) predicts the planar conformation to be the global minimum, with a plateau region near the perpendicular conformation (∼4 kJ/mol higher in energy than the planar conformation). The shape of the curve, and location of minima and barriers, is very dependent on the method and basis set employed. MP2, B3LYP, M05-2X, mPW2-PLYP, and mPW2-PLYP-D (employing basis sets of double- or triple-ζ quality) give results in reasonable agreement with the CCSD(T) results, whereas B3LYP-D and M06-L give vastly overestimated barriers at the perpendicular conformation.

Conformational studies on 2-substituted ethanesulfonates in aqueous solution by 1H NMR spectroscopy and DFT calculations

The conformation of some 2-substituted sodium ethanesulfonates exerting biological functions, XCH 2CH 2SO 3Na (X = S −, Br, Cl, OH, NH 2, SH), has been investigated in aqueous solution by 1H NMR spectroscopy. Potential energy curves for rotation about the C–C bond have been calculated at DFT level of theory (B3LYP/6-311++G(2d,p)) in vacuum and in water (by IEF-PCM method). As concerning dianionic coenzyme M (X = S −), 2-bromo- and 2-chloroethanesulfonate, in vacuum the torsional potential curves and the variations of atomic charges and geometric parameters suggest that electrostatic and steric repulsions between the substituent X and – SO 3 - moiety determine the preference for anti conformer. In isethionate (X = OH), anionic taurine (X = NH 2), and coenzyme M (X = SH), the formation of an intramolecular hydrogen bond stabilizes also gauche-like conformers and the torsional potential curves exhibit two minima. According to Natural Bond Orbital analysis, hydrogen bond can be ascribed to electron transfer from two oxygen lone-pairs of the – SO 3 - moiety to the antibonding Y–H orbital of the substituent X. In all the compounds examined, hyperconjugative interactions tend to stabilize the gauche conformers with respect to the anti one. This means that conformational preferences in vacuum are determined by a counterbalancing of electrostatic, steric, and hyperconjugative interactions. Calculations in vacuum are not in agreement with the experimental conformational behaviour of the compounds examined. In order to reproduce the experimental results at least qualitatively, solvent effect must be introduced.

GLYCAM06: A generalizable biomolecular force field. Carbohydrates

A new derivation of the GLYCAM06 force field, which removes its previous specificity for carbohydrates, and its dependency on the AMBER force field and parameters, is presented. All pertinent force field terms have been explicitly specified and so no default or generic parameters are employed. The new GLYCAM is no longer limited to any particular class of biomolecules, but is extendible to all molecular classes in the spirit of a small-molecule force field. The torsion terms in the present work were all derived from quantum mechanical data from a collection of minimal molecular fragments and related small molecules. For carbohydrates, there is now a single parameter set applicable to both alpha- and beta-anomers and to all monosaccharide ring sizes and conformations. We demonstrate that deriving dihedral parameters by fitting to QM data for internal rotational energy curves for representative small molecules generally leads to correct rotamer populations in molecular dynamics simulations, and that this approach removes the need for phase corrections in the dihedral terms. However, we note that there are cases where this approach is inadequate. Reported here are the basic components of the new force field as well as an illustration of its extension to carbohydrates. In addition to reproducing the gas-phase properties of an array of small test molecules, condensed-phase simulations employing GLYCAM06 are shown to reproduce rotamer populations for key small molecules and representative biopolymer building blocks in explicit water, as well as crystalline lattice properties, such as unit cell dimensions, and vibrational frequencies.

A Computational Study of End‐Group Conformational Energy Barriers in Carotenoids

Introduction Carotenoids possessing different end-groups are known to be selectively metabolized in biological systems and there is evidence demonstrating that end-groups affect the ability of carotenoids to adopt specific geometries within larger biological structures such as membranes. In order to further assess the importance of the end-group structure in carotenoids we have investigated the influence of the end-group type and functionality on the conformational energy barrier. Methods We used the density functional method and the program GAUSSIAN to calculate the conformational energy curves for rotation of the beta-ring or the epsilon-ring relative to short polyene chains around the C6-C7 single bond. Results Epsilon rings have been shown to possess a dramatically larger conformational energy barrier to rotation than beta rings. The rotational energy barrier of the epsilon ring relative to the polyene chain around the C6-C7 bond has been found to range from 8.65 to 9.05 kcal/mole whereas the barrier for rotation around the beta-ring varies from 3.06 to 3.40 kcal/mole. Conclusions Conjugation of the beta-ring has no influence on the conformational energy barrier to rotation in carotenoid systems possessing this end-group. The length of the polyene chain (extent of conjugation) and substitution on the ring have little influence on the rotational energy barrier. The most important factor influencing the conformational energy for ring rotation about the C6-C7 bond is the steric interaction between the ring and polyene methyl groups. The high barrier to rotation for the epsilon ring provides a physical basis for the observed differences in the metabolism and properties of carotenoids possessing this end-group in biological systems.

Density functional study of infinite polyserine chains

Two different helical conformations (alpha and 3-10 helices) of polyserine are studied using density functional theory. The infinite system characterized by exact translational-rotational symmetry is examined in vacuum using the BLYP exchange-correlation functional. Geometry analysis in terms of hydrogen bond strength and total energies of the different conformers are presented. The structural changes due to the presence of the serine side chain are identified comparing the polyserine and polyglycine chains. The rotational energy curves of the side chain are presented for both investigated helices. Band structures of polyserine and polyglycine conformers are also compared.

Ab initio studies on conformation, vibrational and electronic spectra of methyl methacrylate

A systematic quantum mechanical study of the possible conformations, their relative stabilities, vibrational and electronic spectra and thermodynamic parameters of methyl methacrylate (MMA) has been reported for the electronic ground (S 0) and first excited (S 1) states using Density Functional Theory (DFT) with B3LYP functionals and RHF methods in extended basis sets 6-31G, 6-31G**, 6-311G** and 6-311+G** have been conducted. The molecule was considered as a two rotor system having internal rotation about C–C and C–O bonds with the possibility of hindered rotation of the methyl group. Rotation about C–O bond indicates that conformations having the carbonyl and methoxy groups in cis positions are the most stable, while the methyl group has staggered conformation relative to the carbonyl group. Plots of the potential energy curves for rotation about C–C bonds in the S 0 and S 1 states show two energy minima corresponding to the Tc and Cc conformations, separated by 0.365 and 1.104 kcal/mol, respectively, and indicate that the former is more stable than later in both the electronic states. Electronic excitation is found to substantially reduce rotation barrier between the two conformers, which may make their inter-conversion in the S 1 state easier. Fully optimized geometries of the two stable conformers in the S 0 and S 1 states are being reported; the later being reported for the first time. Based on suitably scaled RHF/6-31G** and DFT/6-311G** results, a complete assignment is provided to the fundamental vibrational bands of both the Tc and Cc conformers in terms of frequency, form and intensity of vibrations and potential energy distribution across the symmetry coordinates in the S 0 state. A complete interpretation of the electronic spectra of the Tc and Cc conformers of MMA has been provided by MP2/6-31G** calculations in terms of the nature, energy and intensity of electronic transitions.

A computational study of azine, azoethene, and diimine linkages in the poly/oligoazine system

AbstractHartree‐Fock (HF) and molecular mechanics calculations were performed on linear azine oligomers and model compounds. The rotational energy curves for the model compounds formaldazine, H2C = NN = CH2, ethenyl diazene, H2C = CHN = NH, and ethanediimine, HN = CHCH = NH were calculated for a variety of basis sets at the HF and MP2 level. In all of these cases the rotational energy barriers are quite different from butadienes or aza‐substituted butadienes because of the lone pair–lone pair interaction of the adjacent nitrogen atoms. The results on the model compounds were used to generate a set of molecular mechanics (MM) parameters that are appropriate for linear oligo‐ and polyazines. Comparison of the geometries of the HF results and MM results for the oligoazines showed that the two methods gave comparable results. © 1994 by John Wiley & Sons, Inc.

Ab initio study of conformational behaviour of isopropenylcyclopropane

Analytical gradient (force) methods have been used at the 3-21G basis set level to optimize completely the geometry of isopropenylcyclopropane at each critical point in the potential energy curve for rotation about the CC bond connecting the ring and the isopropenyl group. Similar computations on vinylcyclopropane predicted a gauche—trans conformer equilibrium with the trans conformer more stable than the gauche, in agreement with experiment. For the title compound a gauche—trans equilibrium is also predicted but the relative stabilities of the conformers are reversed: the gauche conformer is predicted to be 2.4 kJ mol −1 more stable than the trans structure. The barriers for the gauche → trans and trans → gauche rotations are predicted to be 11.9 and 9.5 kJ mol −1, respectively, compared to 6.4 and 13.3 kJ mol −1 for the corresponding values in vinylcyclopropane. These differences are attributed mainly to relatively lower steric hindrance in the gauche compared to that in the trans and transition state isopropenylcyclopropane structures. The dipole moments for the trans and gauche optimized conformatio ns are 0.543 and 0.421 D, respectively.

Abinitio study of rotational isomerism in acrolein

Analytic gradient (force) methods at the STO-3G, 3-21G, and 6-31G* basis set levels have been used to optimize the geometry of acrolein completely at each critical point (minima, maximum) in the torsional potential energy curves for rotation about the single C—C bond (dihedral angle θ). The STO-3G and 6-31G* optimizations predict the planar trans conformation (θ = 180°) to be more stable than the cis conformation (θ = 0°) by 1.87 and 6.97 kJ/mol, respectively. The 3-21G optimizations, in disagreement with experiment, place the planar cis structure below the trans by 4.5 J/mol. The predicted relative energy (ΔE) and position for the transition state (TS) for rotation from the trans conformer are ΔE = 22.35, 37.14, and 34.41 kJ/mol and θ = 91.8, 91.6, and 91.0° for the STO-3G, 3-21G, and 6-31G* optimizations, respectively. The computed and experimental geometries, relative energies, dipole moments, and coefficients for the torsional potential expansion are compared.

Ab initio study of rotational isomerism in 1,3-butadiene. Effect 21 of geometry optimization and basis set size on the barriers to rotation and on the stable rotamers

Analytic gradient (force) methods at the STO-3G, 3-21G, 6-31G and 6-31G* basis set levels have been used to optimize the geometry of 1,3-butadiene at each critical point (minima, maxima) in the torsional potential energy curves for rotation about the central CC bond (dihedral angle θ). Each CHCH 2 group was constrained planar and the effect of this geometry constraint was investigated by additional STO-3G and 3-21G optimizations. The planar trans conformation (θ = 180°) is predicted to be most stable, in agreement with experiment. Small variations in the predicted relative energy (Δ E) and in the position of the transition state (TS) for rotation from the trans position are observed: Δ E = 23.5, 23.6, 25.9 and 25.4 kJ mol −1 and θ = 95.0, 101.8, 101.6 and 101.5° for the STO-3G, 3-21G, 6-31G and 6-31G* basis set optimizations, respectively. The STO-3G optimizations predict an energy minimum for the planar cis conformation (θ = 0°), 7.7 kJ mol −1 above the trans minimum. All three larger basis sets predict a maximum for the cis structure, with small gauche—gauche rotational barriers (2.0–4.1 kJ mol −1, the largest value corresponding to optimizations with the 3-21G basis set and non-planar CHCH 2 groups). The gauche minimum is predicted to lie 11.3–13.2 kJ mol −1 above the trans, at θ's in the range 35.5–38.5°. The positions and relative energies of the critical points in the torsional potential energy curves predicted by the 3-21G, 6-31G and 6-31G* optimizations are in good agreement with those proposed by Durig, et al. [1] to reproduce the Raman overtone spectrum of 1,3-butadiene for a gauche—trans rotamer equilibrium. A series of 6-31G** computations with the optimized geometries from the smaller basis sets indicates that optimization at the 6-31G** basis level would give results similar to those obtained with the above three split-valence basis sets.

An ab initio study of some structural features and the rotational barriers in performic acid, formic acid and hydrogen peroxide

Calculations on performic acid at the 4-31G level, with and without bond functions with complete geometry optimization, and at the (9, 5) level, with and without polarization functions and rigid rotation, all give no sign of a well in the potential energy curve for rotation about the O/O bond axis in the region of 50° – 90° ; and all but the unaugmented 4-31G basis set find the cis- cis planar conformer to be the most stable form. Calculations at the (9,5) level with rigid rotation find the energies of the other planar conformers, relative to the cis- cis conformer, to be 0.94, 1.50 and 14.80 kcal mol −1 for the trans- trans, cis- trans and trans- cis structures respectively. These energies and also that for the barrier separating the cis- cis and cis- trans conformers, 1–2 kcal mol −1, are discussed in relation to corresponding data for formic acid, hydrogen peroxide and several planar four heavy-atom molecules. Dipole moment calculations using the same basis sets would seem to favor a skew conformation as the most stable for performic acid, but comparisons between calculated and experimental values for formic acid and for hydrogen peroxide cast doubt on the validity of such results.

Conformational structure of glycerol trivalerate and its relation to phospholipids: Studies by NMR and potential energy calculations

The structure of a model lipid (glycerol trivalerate, GTV) has been investigated by 1H and 13C NMR, and energy calculations based on classical potential functions (CPF). The structure of glycerol-ester pivot in GTV is characterized by a dynamic equilibrium between two dominant conformations. One of the two conformations (SA) is similar to the reported crystal structure of triglycerides β-triaurin and β-tricaprin and has the following conformational angles: θ 1 = 52°, θ 3 = 46°, α 1 = 208°, β 1 = 156° and γ 1 = 186° . The other conformer (SB) is similar to the reported crystal structure of β and γ chains in 1,2- dilauroyl-D,L- phosphatidylethanolamine and has the conformational angles: θ 1 = 287°, θ 3 = 155°, α 1 = 195°, β 1 = 85° and γ 1 = 194° . The ester groups acquire a rigid planar conformation ( α 2, β 2, γ 2 = 180° ), while the potential energy curves for rotation around the chemical bonds OCOCCC( α 3, β 3 and γ 3 ) indicate a high degree of flexibility. The hydrocarbon chains show a distribution of the gauche and trans conformations around CCCC bonds with a preference for the trans arrangement by almost 0.8 kcal/mol. The conformational picture of the hydrocarbon chains and glycerol moiety in GTV is very similar to that in phospholipids. These results indicate caution in using the reported crystal structure of 1,2- dilauroyl-D,L- phosphatidylethanolamine as the only model for the organization of lipid molecules in biological membranes.

ChemInform Abstract: NONBONDED ATTRACTION IN METHYL VINYL ETHER

AbstractMO‐Berechnungen ergeben die Existenz von zwei stabilen Konformeren.

EHT conformational study of nicotinamide and related amides

EHT rotational energy curves are presented for various nicotinamides and benzamide. The conformations calculated for nicotinamide and benzamide are comparable to those determined by X-ray methods. Protonation, N-methyl substitution and the introduction of a ring nitrogen meta to the amide group are discussed in terms of the corresponding calculated effect on the rotational energy curves. Some implications for the conformation of NAD⊕ are presented.

Visual pigments: their spectra and isomerizations.

Abstract— We have made Pariser‐Parr‐Pople molecular orbital calculations of the torsional energy curves for rotation about pertinent bonds in retinal and its Schiffs base derivatives. The results correlate well with their observed spectra and isomerization behavior. The calculations are also consistent with the visual pigment model of a protonated Schiffs base of retinal perturbed by a charged group in its environment.