Function Of Dihedral Angle Research Articles

Computation of global reactivity descriptors and first hyper polarisability as a function of torsional angle of donor–acceptor substituted biphenyl ring system

ABSTRACTGlobal reactivity descriptors, e.g. average polarisabilty (αav), chemical hardness (η), electrophilicity index (ω) of two donor–acceptor substituted biphenyl, i.e. Dimethyl-(4ʹ-Nitro-biphenyl-4-yl)-amine (NBA) and 4ʹ-Dimethylamino-biphenyl-4carbonitrile (DBC), were computed along the torsional potential of two biphenyl ring systems. Density functional-based hybrid functional B3LYP with 6-31G(d) basis were used to all the computational study. It is observed that variation of the global reactivity descriptors η, ω as a function of torsional angle of biphenyl ring of NBA are in accordance with the maximum hardness and minimum electrophilicity principle. But the variations of αav, η, ω for DBC and αav for NBA are not in accordance with the respective extremum principles. These apparent violations of extremum principles have been explained as the non-constancy of external potential within the tolerance limit for the respective parameters during the variation of torsional angle. The variation of first hyperpolarisability (βav) as a function of dihedral angle has been explained with the extent of charge transfer character of conformers for both NBA and DBC. It is also observed that the variation of first hyper polarisability is a function of S0 − S1 optical energy gap rather than HOMO–LUMO gap of the titled compounds.

Comparative study of 3D-RISM theory and molecular dynamics calculations for the free-energy landscape of a hydrated dipeptide

In the present study, the free-energy landscape of a hydrated alanine dipeptide has been studied by the 3D-RISM theory. We calculate the hydration free energy as a function of dihedral angles and using both the 3D-RISM theory and the umbrella sampling method. The 3D-RISM results are found to be in good agreement with those by the umbrella sampling calculations, demonstrating the reliability of the integral equation theory applied to bimolecular systems.

Electronic Transitions in Conformationally Controlled Peralkylated Hexasilanes.

The photophysical properties of oligosilanes show unique conformational dependence due to σ-electron delocalization. The excited states of the SAS, AAS, and AEA conformations of peralkylated n-hexasilanes, in which the SiSiSiSi dihedral angles are controlled into a syn (S), anti (A), or eclipsed (E) conformation, were investigated by using UV absorption, magnetic circular dichroism (MCD), and linear dichroism spectroscopy. Simultaneous Gaussian fitting of all three spectra identified a minimal set of transitions and the wavenumbers, oscillator strengths, and MCD B terms in all three compounds. The results compare well with those obtained by using the symmetry-adapted-cluster configuration interaction method and almost as well with those obtained by time-dependent density functional theory with the PBE0 functional. The conformational dependence of the transition energies and other properties of free-chain permethylated n-hexasilane, n-Si6 Me14 , was also examined as a function of dihedral angles, and the striking effects found were attributed to avoided crossings between configurations of σσ* and σπ* character.

ChemInform Abstract: Triplet-State Features of 2,2′-Biquinoline and Derivatives

The authors have investigated, by optically detected magnetic resonance, the triplet-state zero-field characteristics of a series of annelated 2,2{prime}-biquinoline derivatives. These systems have their 3,3{prime}-positions joined by a bridge consisting of 1, 2, 3, or 4 methylene units, resulting in a relative dihedral geometry between the quinoline chromophore planes that varies from coplanar to about 58 degrees. Previous accounts in the literature have reported the existence of two types of excited triplet states in 2,2{prime}-biquinoline: an excitation that is localized on one of the quinoline moieties and one that is delocalized over the entire biquinoline double molecule. In determining the relative apportionment of these triplet states as a function of dihedral angle, they found only one triplet state to be present in each of the compounds investigated. Subsequent ODMR reinvestigation of the parent compound 2,2{prime}-biquinoline produced results consistent with those obtained for the annelated biquinoline derivatives. It was concluded that this triplet-state photoexcitation is constrained on one of the quinoline moieties only.

Dynamics and mechanism of the Crystal II → smecticG phase transition in TB7A by a temperature‐dependent micro‐Raman study and DFT calculations

AbstractThe solid to smecticG (SmG) phase transition in a Schiff base liquid crystalline compound, terepthal‐bis‐heptylaniline (TB7A), is monitored in situ by temperature‐dependent Raman microspectroscopy, using the band of a CH in‐plane bending mode as a marker. Contrary to the earlier report of a sudden wavenumber shift, the in situ measurement shows very clearly that a new Raman band at ∼1160 cm−1 appears at the Crystal II → SmG transition. The dynamics of this phase transition is discussed in terms of a triple well potential below 210 K and a double well potential above 210 K. The phase transition essentially takes place as a result of intra‐molecular rotation about the long molecular axis. The optimization energy at various fixed dihedral angles, (CCCN) are calculated using density functional theory (DFT) at the B3LYP/6‐31G* level of theory. The relative energy at each dihedral angle is calculated relative to optimization energy obtained without any constraints and plotted as a function of dihedral angle (Φ) between the adjacent phenyl ring planes, which also shows a double well potential at room temperature. Copyright © 2009 John Wiley & Sons, Ltd.

The Synthesis of N-Benzyl-2-azanorbornene via Aqueous Hetero Diels–Alder Reaction. An Undergraduate Project in Organic Synthesis and Structural Analysis

The synthesis of N-benzyl-2-azanorbornene via aqueous hetero Diels�Alder reaction of cyclopentadiene and benzyliminium chloride formed in situ from benzylamine hydrochloride and formaldehyde is described. Characterization of the product was achieved by IR and NMR spectroscopies. The spectral data acquired are thoroughly discussed. Numerous coupling constants were extracted from the 1H NMR spectrum. They provide a valuable material to familiarize students with the different types of proton�proton coupling patterns and their typical ranges. Karplus type correlations served to calculate 3J vicinal coupling constants as a function of dihedral angles. These computational studies involved molecular modeling. Because the synthetic part is rather straightforward and easy to carry out, this experiment is suitable for an introductory laboratory course where it can serve to illustrate the concepts of green chemistry and atom efficiency. Emphasis can also be placed on structural analysis for use within a spectroscopy course even if there is no activity component associated with it. Last but not least, the whole project provides ample materials for an advanced undergraduate laboratory in green chemistry that combines organic synthesis, structural analysis, and theoretical calculations.

Vicinal Deuterium Perturbations on Hydrogen NMR Chemical Shifts in Cyclohexanes

The substitution of a deuterium for a hydrogen is known to perturb the NMR chemical shift of a neighboring hydrogen atom. The magnitude of such a perturbation may depend on the specifics of bonding and stereochemical relationships within a molecule. For deuterium-labeled cyclohexanes held in a chair conformation at -80 degrees C or lower, all four possible perturbations of H by D as H-C-C-H is changed to D-C-C-H have been determined experimentally, and the variations seen, ranging from 6.9 to 10.4 ppb, have been calculated from theory and computational methods. The predominant physical origins of the NMR chemical shift perturbations in deuterium-labeled cyclohexanes have been identified and quantified. The trends defined by the Delta delta perturbation values obtained through spectroscopic experiments and by theory agree satisfactorily. They do not match the variations typically observed in vicinal J(H-H) coupling constants as a function of dihedral angles.

Molecular Orbital and Density Functional Study of the Formation, Charge Transfer, Bonding and the Conformational Isomerism of the Boron Trifluoride (BF3) and Ammonia (NH3) Donor-Acceptor Complex

The formation of the F3B–NH3 supermolecule by chemical interaction of its fragment parts, BF3 and NH3, and the dynamics of internal rotation about the ‘B–N’ bond have been studied in terms of parameters provided by the molecular orbital and density functional theories. It is found that the pairs of frontier orbitals of the interacting fragments have matching symmetry and are involved in the charge transfer interaction. The donation process stems from the HOMO of the donor into the LUMO of the acceptor and simultaneously, back donation stems from the HOMO of acceptor into the LUMO of the donor. The density functional computation of chemical activation in the donor and acceptor fragments, associated with the physical process of structural reorganization just prior to the event of chemical reaction, indicates that BF3 becomes more acidic and NH3 becomes more basic, compared to their separate equilibrium states. Theoretically it is observed that the chemical reaction event of the formation of the supermolecule from its fragment parts is in accordance with the chemical potential equalization principle of the density functional theory and the electronegativity equalization principle of Sanderson. The energetics of the chemical reaction, the magnitude of the net charge transfer and the energy of the newly formed bond are quite consistent, both internally and with the principle of maximum hardness, PMH. The dynamics of the internal rotation of one part with respect to the other part of the supermolecule about the ‘B–N’ bond mimics the pattern of the conformational isomerism of the isostructural ethane molecule. It is also observed that the dynamics and evolution of molecular conformations as a function of dihedral angles is also in accordance with the principle of maximum hardness, PMH. Quite consistent with spectroscopic predictions, the height of the molecule’s barrier to internal rotation is very small. A rationale for the low height of the barrier has been put forward in terms of the energy partitioning analysis. On the question of origin of the barrier to internal rotation, we conclude that the conformational barrier to internal rotation does not originate from a particular region of the molecule, but rather it is a result of the subtle conjoint interplay of a number of opposing effects of one- and two-center bonded and nonbonded energy terms involving the entire skeleton of the molecule.

Local propensities and statistical potentials of backbone dihedral angles in proteins.

The following three issues concerning the backbone dihedral angles of protein structures are presented. (1) How do the dihedral angles of the 20 amino acids depend on the identity and conformation of their nearest residues? (2) To what extent are the native dihedral angles determined by local (dihedral) potentials? (3) How to build a knowledge-based potential for a residue's dihedral angles, considering the identity and conformation of its nearest residues? We find that the dihedral angle distribution for a residue can significantly depend on the identity and conformation of its adjacent residues. These correlations are in sharp contrast to the Flory isolated-pair hypothesis. Statistical potentials are built for all combinations of residue triplets and depend on the dihedral angles between consecutive residues. First, a low-resolution potential is obtained, which only differentiates between the main populated basins in the dihedral angle density plots. Minimization of the dihedral potential for 125 test proteins reveals that most native alpha-helical residues (89%) and a large fraction of native beta-sheet residues (47%) adopt conformations close to their native one. For native loop residues, the percentage is 48%. It is also found that this fraction is higher for residues away from the ends of alpha or beta secondary structure elements. In addition, a higher resolution potential is built as a function of dihedral angles by a smoothing procedure and continuous functions interpolations. Monte Carlo energy minimization with this potential results in a lower fraction for native beta-sheet residues. Nevertheless, because of the higher flexibility and entropy of beta structures, they could be preferred under the influence of non-local interactions. In general, most alpha-helices and many beta-sheets are strongly determined by the local potential, while the conformations in loops and near the end of beta-sheets are more influenced by non-local interactions.

DYNAMIC SOLVENT EFFECT ON THE ISOMERIZATION OF 2-ALKENYLANTHRACENE

Dynamic solvent effect on the isomerization of two 2-alkenylanthracene derivatives in the lowest excited singlet (S1) state was investigated. The isomerization rates were determined in supercritical fluids (SCF) and in a series of compressed liquid n-alkane solvents. Kramer's turnover behavior was observed. The maximum rate is substantially smaller than expected from transition state theory. Torsional potentials between anthracene ring and alkene plane for the isomerization reaction coordinate of 2-alkenylanthracene were calculated by ab initio method as a function of dihedral angle. It was confirmed by the calculation that the isomerization followed by experiment is from s-trans to s-cis conformers.

Ab initio calculation of the torsional potential for 2-alkenylanthracene in the ground and excited states

Torsional potentials between the anthracene ring and alkene planes for two 2-alkenylanthracene derivatives both in the ground- and excited-states were calculated using ab inito method as a function of dihedral angle. Molecular geometries were optimized at the restricted Hartree–Fock level in the ground-state, whereas in the excited-state at the level of configuration interaction with single excitation. In the ground-state it is s- trans conformation that is more stable and more planar. While in the excited-state both are planar and the potential shape is more like symmetrical for 2-vinylanthracence, although somewhat distorted for 2-(2 ′ propenyl) anthracene. Stabilization energies, barrier energies, and barrier top frequencies of both ground- and excited-states were determind

Molecular optical rotation: an evaluation of semiempirical models

Ab initio optical rotations have been obtained for allene, 1,3-dichloroallene, H 2O 2, and H 2S 2 as a function of dihedral angles, both at SCF and post-SCF levels. The results have been used to test (a) the concept that the molecular optical rotation can be written as a ∑ i M i sin θ i , where θ i is the dihedral angle of the ith X–A–A–X type segment and M i is a parameter associated with that segment; and (b) Kirkwood's polarizability model. The predicted ab initio optical rotation was found to depend strongly on the level of ab initio theory used, so highest levels of theory are required for accurate predictions. The optical rotation patterns obtained using high-level ab initio theory for H 2O 2, H 2S 2 and allene, as a function of dihedral angles, are found to be in line with Kirkwood's polarizability model predictions but not with the ∑ i M i sin θ i predictions.

Ab initio theoretical optical rotations of small molecules

Abstract Optical rotations of small chiral molecules have been calculated ab initio to evaluate the role of substituents and of conformations. The optical rotations of oxaziridines provide a nice correlation between the sign of optical rotation and absolute configuration. Such correlation is not obvious in the case of diaziridines and tetrahydrofurans. The optical rotations obtained for different conformers of 3-butyn-2-ol suggested a possible predominant conformation in liquid solutions. The prediction of optical rotations, as a function of dihedral angle, for H 2 O 2 and H 2 S 2 reveal that the sign of optical rotation is negative for counter-clockwise dihedral angles (M-helicity) and the magnitude is maximum at a dihedral angle of 90° (in H 2 O 2 ) or 110° (in H 2 S 2 ).

Nonlinear dynamics of molecular systems and the correlations of internal motions in oligopeptides

The dynamical properties of significantly nonlinear molecular systems with conformational mobility are discussed. The peculiarities of the figurative point movements along the potential energy hypersurfaces with a lot of saddle points are investigated. The methods of dynamical correlation functions of dihedral angles and calculation of free energy maps are developed. These correlation functions and free energy maps can characterize the dynamical properties of the nonlinear systems in detail. The dynamical properties of some oligopeptides are described.

Triplet-state features of 2,2'-biquinoline and derivatives

The authors have investigated, by optically detected magnetic resonance, the triplet-state zero-field characteristics of a series of annelated 2,2{prime}-biquinoline derivatives. These systems have their 3,3{prime}-positions joined by a bridge consisting of 1, 2, 3, or 4 methylene units, resulting in a relative dihedral geometry between the quinoline chromophore planes that varies from coplanar to about 58 degrees. Previous accounts in the literature have reported the existence of two types of excited triplet states in 2,2{prime}-biquinoline: an excitation that is localized on one of the quinoline moieties and one that is delocalized over the entire biquinoline double molecule. In determining the relative apportionment of these triplet states as a function of dihedral angle, they found only one triplet state to be present in each of the compounds investigated. Subsequent ODMR reinvestigation of the parent compound 2,2{prime}-biquinoline produced results consistent with those obtained for the annelated biquinoline derivatives. It was concluded that this triplet-state photoexcitation is constrained on one of the quinoline moieties only.

Uncertainties in structural determinations of oligosaccharide conformation, using measurements of nuclear Overhauser effects

A fundamental problem in the determination of molecular structure by n.m.r. spectroscopy is insufficient experimental constraints. This problem is particularly marked for oligosaccharides, where few constraints are available across glycosidic linkages. By calculating distances as a function of dihedral angle, it is shown that, in general, two n.O.e. constraints result in two possible conformations for each glycosidic linkage, one of which can usually be discarded on the basis of model building or energy calculations. Using these calculations, an estimate of the uncertainty in the structure can be obtained.

Dynamics of peptides with fixed geometry: Kinetic energy terms and potential energy derivatives as functions of dihedral angles

AbstractExpressions are derived for computing the kinetic energy of a peptide with fixed geometry, in terms of dihedral angles as generalized coordinates; other expressions required for the solution of Lagrange's equations are also presented. The peptide is regarded as held stationary at one end. We also outline the computations that are needed in calculating the components of the third derivative of a potential energy function that consists of a sum of pairwise interatomic interactions.

Interplay of Sintering Microstructures, Driving Forces, and Mass Transport Mechanisms

The equilibrium shapes of segments of a row of sintering particles are calculated for the case where interparticle distances are constrained and, in particular, for only vapor‐phase transport or surface diffusion active. These equilibrium states are contrasted with those obtained by mechanisms which allow densification. The sintering potentials and surface curvatures are calculated for the equilibrium shapes as a function of dihedral angle. Expressions for the rate of shrinkage are presented and, for the case of equilibrium structures, calculated exactly.

Metal-support interaction: (μ-H)(μ-OSiEt3)Os3(CO)10, A molecular analogue of a surface complex and the computer modelled surface structures of (μ-H)(μ-OSi)Os3(CO)10 and (μ-OSi)2Os3(CO)10

Metal-support interaction involving the surface complex formed from the reaction of silica with Os3(CO)12 at 150°C has been modelled employing computer graphics and molecular mechanics techniques. This surface complex is generally represented as (μ-H)(μ-Osi) Os3(CO)10 (I), with a surface oxygen bridging two osmium atoms. However, a second arrangement with two surface oxygens bridging the same two osmium atoms, (μ-Os)2Os3(CO)10 (II), has also been considered. A computer model has been developed for partially hydroxylated silica surface. Employing structural parameters from model compounds, metal-support interaction of the cluster fragments (μ-H)Os3(CO)10 and Os3(CO)10 with surface oxygens to form surface complexes I and II was studied using energy minimization techniques and considering non-bonded contacts as a function of dihedral angle. The results clearly indicate that the cluster fragment Os3(CO)10 will not fit on the silica by means of a double oxygen bridge to two osmium atoms to give complex II; however, the (μ-H)Os3(CO)10 fragment will bind to selected oxygen sites of the silica without steric restraint to form complex I.

A NON-SYMMETRICAL DIESTER OF 1(R)-AMINO-1-PHENYLMETHANEPHOSPHONIC ACID. PART II. THE DETERMINATION OF ABSOLUTE CONFIGURATION AT THE CHIRAL PHOSPHORUS CENTER BY1H NMR STUDIES

Abstract The diastereoisomers of the ethyl-2,2,2-trichloroethyl diester of optically active 1-amino-1-phenylmethanephosphonic acid derivatives were examined by 1H NMR and IR methods. The configuration of the phosphorus atom in each diastereoisomer was determined on the basis of conformational analysis using 1H NMR spectra. Calculations of the location of the methylene protons in the trichloroethyl group as a function of dihedral angles were performed and compared with the experimental values.