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We report on the structures of two conformers of 2-thiophenecarboxaldehyde as obtained using a combination of molecular jet Fourier-transform microwave spectroscopy and quantum chemical calculations. The microwave spectrum was recorded using two spectrometers operating in the frequency ranges of 2.0 to 26.5 GHz and 26.5 to 40.0 GHz. The spectra of all singly-substituted heavy atom isotopologues 13C, 18O and 34S in their natural abundances could be measured and assigned to determine the gas-phase substitution rs and semi-experimental r e SE structures of the most abundant conformer. The spectrum of the 33S isotopologue with its nuclear quadrupole coupling hyperfine structure was analysed, yielding the complete quadrupole tensor with high accuracy. The experimental results are used to map the observed rotational constants to the corresponding molecular structure obtained from quantum chemical calculations, which predicted two conformers with an energy difference of about 6 kJ mol−1 at the MP2/6-311++G(d,p) level of theory. Insight into the conformational stability of aromatic heterocyclic carboxaldehydes and bond situations of the sulfur atom extracted from the hyperfine structure of the 33S nucleus are discussed within the frame of the current literature. This work provides an important contribution to the study and characterisation of sulfur-containing volatile organic compounds. [ABSTRACT FROM AUTHOR]

The conformational study using Potential Energy Surface analysis was performed and its minimum energy conformer has been obtained for N-(2-(Trifluoromethyl)phenyl)acetamide. Fourier Transform Infrared and Fourier Transform Raman investigation have been done experimentally and theoretically. Nuclear Magnetic Resonance analysis has been performed to obtain 1H and 1C chemical shifts. Ultraviolet-Visible analysis has been performed to obtain maximum absorption wavelength. The molecular orbital diagram with different energies has been obtained and compared with the band gap of Ultraviolet-Visible data. Wave function analysis has been discussed to know the electronic properties. Thus, this present study reports the structural, electrical, chemical activities of the title compound. [ABSTRACT FROM AUTHOR]

The C-alkylpyrogallol[4]arene macrocycles are known to form self-assembled dimeric and hexameric nanocapsules. Several conformations of alkyl-substituted pyrogallol[4]arenes have been found to be thermodynamically stable, with the most stable structures typically being a chair and cone. However, experimental evidence suggests that aryl-substituted pyrogallol[4]arenes exist in the chair conformation, implying that because for nanocapsule formation the cone is the necessary conformer of the subunits of these capsules, the chair must undergo some transition to the cone. To benchmark the intrinsic behavior of these systems, we here use quantum chemical calculations and molecular dynamics simulations to (1) investigate conformers of the R=H system and their solvent interactions to understand the structures and their relative stabilities, (2) explore interconversions between conformers, and (3) gain preliminary insight into the mechanism by which self-assembly of the nanocapsule occurs. [ABSTRACT FROM AUTHOR]

The C-alkylpyrogallol[4]arene macrocycles are known to form self-assembled dimeric and hexameric nanocapsules. Several conformations of alkyl-substituted pyrogallol[4]arenes have been found to be thermodynamically stable, with the most stable structures typically being a chair and cone. However, experimental evidence suggests that aryl-substituted pyrogallol[4]arenes exist in the chair conformation, implying that because for nanocapsule formation the cone is the necessary conformer of the subunits of these capsules, the chair must undergo some transition to the cone. To benchmark the intrinsic behavior of these systems, we here use quantum chemical calculations and molecular dynamics simulations to (1) investigate conformers of the R=H system and their solvent interactions to understand the structures and their relative stabilities, (2) explore interconversions between conformers, and (3) gain preliminary insight into the mechanism by which self-assembly of the nanocapsule occurs. [ABSTRACT FROM AUTHOR]

A pulsed molecular beam Fourier transform microwave spectrometer operating in the frequency range 2–26.5 GHz was used to measure the spectrum of phenetole (ethyl phenyl ether or ethoxybenzene, C6H5OC2H5). The conformational landscape is completely determined by the orientations of the phenyl ring and the ethyl group. A two-dimensional potential energy surface was calculated at the MP2/6-311++G(d,p) level of theory. Two conformers were found: thetransconformer has aCssymmetry, and thegaucheconformer has the ethyl group tilted out of the phenyl plane by about 70°. Totally, 186 rotational transitions were assigned to the more stable planartransconformer, and fitted using a semi-rigid rotor model to measure accuracy. Highly accurate rotational and centrifugal distortion constants were determined. Several method and basis set combinations were applied to check for convergence and to compare with the experimentally deduced molecular parameters. [ABSTRACT FROM AUTHOR]

In order to facilitate its detection in astronomical observations, the measurement of the rotational spectrum of acrylic acid has been extended to 397 GHz using a free space cell at room temperature. 295 new lines were assigned to thes-cisconformer and 286 new lines to thes-transconformer of acrylic acid. Using the determined experimental parameters, the predictions of the rotational transition frequencies up to 900 GHz and their intensities were obtained at temperatures of 100 and 200 K and at room temperature. Based on these predictions, a search of the most intense transitions of acrylic acid in star-forming regions was performed using published data from the HERSCHEL Science Archive. No lines were found but the possibility of observing rotational transitions of acrylic acid in astronomical objects is discussed. [ABSTRACT FROM AUTHOR]

Fischer aminocarbene complexes [(CO)5M=C(NHR)Y] (M=Cr or W; R=H, Cy or C2H4NH2; Y=2-thienyl or 2-furyl) containing an amino group exist as two isomers in solution, theEandZisomers. The two isomers arise from restricted rotation about the N–Ccarbenebond, that exhibits double bond character due toπ-donation from nitrogen to the carbene carbon. Each isomer exists as two conformers in fast equilibrium with each other. The conformers arise from the rotation of the aryl ring around the Ccarbene–Carylsingle bond with a DFT calculated rotation barrier of 0.1–0.5 eV. The main isomer, isolated in the solid state, generally exhibits asynorientation of the aryl ring relative to the amino substituent and aZconfiguration of the amino substituent relative to the metal. [ABSTRACT FROM PUBLISHER]

In this study, the influences of initial settings, i.e. initial conformations, configurations and docking parameters, on docking results were investigated. The conformations used in the study were generated by the CAMDAS program. After the conformational search calculations, five structures were selected from the conformer groups according to their conformation energies and root mean square deviations against crystal structures; for example, the lowest energy conformer, as well as the closest and farthest conformers to the crystal structure, was retrieved. Several docking parameter settings were used (default, high speed, generating 50 poses). In this study, docking calculations were conducted using the GOLD, eHiTS, AutoDock, AutoDock vina, FRED and DOCK programs. The success rates of GOLD, eHiTS and FRED were better than those of AutoDock, AutoDock vina and DOCK. The docking results using the farthest conformations were worse than those obtained using other conformations, indicating that some conformation search for the ligand molecule should be performed before the docking calculations. [ABSTRACT FROM AUTHOR]

Density functional theory using the B3LYP/6-311++G** method was employed to calculate the details of the electronic structure and electronic energy of the carbonic anhydrase enzyme active center (CA); topiramate, a sulfamate substituted monosaccharide; and the complex between topiramate and CA. The calculated results indicate that topiramate appears to adopt a twist-boat conformation in the solution. The conformational analysis around the S-N bond (H-N-S-O dihedral angle) in deprotonated topiramate shows that the conformers with a H-N-S-O torsion of 270, 0, and 180 degrees are the minimum, transition state, and maximum energy conformers, respectively. The deprotonated form of topiramate is coordinated to the Zn2+ion. [ABSTRACT FROM PUBLISHER]

It is well known that guinea pig β2adrenoceptors (Gβ2ARs) and human β2adrenoceptors (Hβ2ARs) have structural similarity. However, only one conformational state of Gβ2ARs has been studied – the putative inactive state. As adrenoceptors have a repertoire of conformations, and there is evidence that a certain conformation is stabilised as a ligand approaches, the aim of this study was to build four models of Gβ2ARs by using putative active/inactive Hβ2AR conformers as a template. We evaluated the accuracy of these models in regard to the binding mode and affinity values of a set of known β2AR ligands through docking and molecular dynamics simulations. During docking simulations, ligands reached Gβ2AR sites similar to those reported for Hβ2ARs. The greatest differences between conformational states were found in the domains (TM5 and TM6) previously suggested as being key to ligand recognition. The coefficients of determination between experimental and calculated affinity values were near to but less than 0.66 in all cases. The highest values were for agonists on the active models and antagonists on the inactive model. The four Gβ2AR models proved useful for analysing agonist/antagonist activity. The results suggest that the selection of an adequate model is dependent on the intrinsic activity of a given ligand. [ABSTRACT FROM AUTHOR]

Hydrogen bonding is one of the most important and ubiquitous interactions present in Nature. Several studies have attempted to characterise and understand the nature of this very basic interaction. These include both experimental and theoretical investigations of different types of chemical compounds, as well as systems subjected to high pressure. The O–H..O bond is of course the best studied hydrogen bond, and most studies have concentrated on intermolecular hydrogen bonding in solids and liquids. In this paper, we analyse and characterise normal hydrogen bonding of the general type, D–H...A, in intramolecular hydrogen bonding interactions. Using a first-principles density functional theory approach, we investigate low energy conformers of the twenty α-amino acids. Within these conformers, several different types of intramolecular hydrogen bonds are identified. The hydrogen bond within a given conformer occurs between two molecular groups, either both within the backbone itself, or one in the backbone and one in the side chain. In a few conformers, more than one (type of) hydrogen bond is seen to occur. Interestingly, the strength of the hydrogen bonds in the amino acids spans quite a large range, from weak to strong. The signature of hydrogen bonding in these molecules, as reflected in their theoretical vibrational spectra, is analysed. With the new first-principles data from 51 hydrogen bonds, various parameters relating to the hydrogen bond, such as hydrogen bond length, hydrogen bond angle, bond length and vibrational frequencies are studied. Interestingly, the correlation between these parameters in these bonds is found to be in consonance with those obtained in earlier experimental studies of normal hydrogen bonds on vastly different systems. Our study provides some of the most detailed first-principles support, and the first involving vibrational frequencies, for the universality of hydrogen bond correlations in materials. [ABSTRACT FROM AUTHOR]

The polarities of bis(2-phenylethyl) and bis(2-phenylpropyl) phosphine selenides were determined and conformational analysis of these phosphine selenides was carried out by the method of dipole moments, IR spectroscopy, and quantum chemical calculations. They exist as an equilibrium of several conformers, and the preferred conformers have gauche orientation of the P = Se and Csp3– Csp3bonds. [ABSTRACT FROM PUBLISHER]

A new macrocyclic compound, [Ni(L)](ClO4)2(1) (L = 1,3,10,12,15,18-hexaazatetracyclo [16,2,1,112.15,04.9]docosane) was synthesized by condensation reactions involving amines and formaldehyde in the present of nickel anion. Compound 1 crystallizes in monoclinic, space groupCc, witha= 13.802(11) Å,b= 12.975(10) Å,c= 13.322(11) Å,α= 90°,β= 99.439(9)°,γ= 90°,V= 2353(3) Å3,Z= 4,F(000) = 1184,Dc= 1.598 Mg/m3,Mr= 566.09,μ= 1.106 mm−1,λ= 0.71073 Å, the finalR= 0.0425 andωR= 0.1235 for 2,030 observed reflections withI>2σ(I). X-ray crystallographic analysis shows simultaneous presence of two conformers of the same macrocyclic compound [Ni(L)]2+in the crystal. [ABSTRACT FROM AUTHOR]

The present study deals with a non-native amino acid,cis-4-hydroxy-d-proline (CHDP) using density functional theory at B3LYP/6-31+G(d,p) level. The potential energy surface scan reveals the global minimum structure of CHDP along with two potential conformers. Highest occupied molecular orbital, lowest unoccupied molecular orbital, and molecular electrostatic potential surfaces are used to explain the chemical reactivity of title molecule. The atomic charge analysis has been carried out using Mulliken and natural population schemes. The equilibrium geometry of CHDP dimer has been obtained and inter-molecular interactions are explored using QTAIM and Natural bonding orbital analyses. Vibrational spectroscopic analysis has been performed on CHDP monomer and dimer at the same level of theory. Assignments to all vibrational modes up to 400 cm−1have been offered along with their potential energy distribution to the maximum possible accuracy. The calculated frequencies are scaled by an equation, rather than by a constant factor and then compared with experimental FT-IR frequencies obtained by KBr disc and Nujol mull techniques. A number of electronic and thermodynamic parameters have also been evaluated for CHDP monomer and dimer. [ABSTRACT FROM PUBLISHER]