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The crystal structures of the oxidized states of three of the most common biochemical reducing agents have been determined, by crystallization from aqueous solution where possible: tris(2-carboxyethyl)phosphine oxide (TCEP oxide, 1), bis(2-hydroxyethyl) disulfide (2MESS, 3), and tributylphosphine oxide (Bu 4 PO, 4). In addition, a less disordered crystal structure of the reducing agent tris(2-carboxyethyl)phosphonium chloride (TCEP·HCl, 2) has been obtained. A greatly simplified method was found for synthesizing 1. An unusual method of obtaining X-ray quality crystals from hard-to-crystallize oily liquids is described, in which the oil is solidified to a glass by rapid cooling, allowed to warm to a supercooled liquid containing a few seed crystals, and finally crystallized just below its melting point. This method was successfully used to crystallize 3 , a viscous oil at room temperature that had resisted all other methods of crystallization, for X-ray diffraction. An ab initio quantum chemical analysis of the conformers of 3 showed that the molecular geometry of this flexible molecule in the solid state was 320 kJ/mol higher than that of the lowest-energy conformer, underscoring the fact that the solid-state structure may not always yield the same molecular geometry as that of the minimum-energy conformer, especially for flexible molecules with strong intramolecular nonbonding interactions. The unusual NMR spectral characteristics of 4 are elucidated. • Crystal structures of oxidized states of some common biochemical reducing agents. • One of our structures reveals marked differences from the ab initio DFT geometry. • We have rationalized odd spectral features found when examining these molecules. • Our structures will help identify possible contaminants in protein crystallization. • We disclose an unusual method of growing X-ray quality crystals of intractable oils. [ABSTRACT FROM AUTHOR]

• The biological activities of the stereoisomers of dipeptidyl boron derivatives were successfully distinguished for the first time. • EC-GA method is capable of distinguishing between the stereoisomers including both enantiomers and diastereomers. • The compound 99 which is the diastereomer of 27 is a promising candidate for future studies of more potent proteasome inhibitors. The electron conformational genetic algorithm (EC-GA) method had been employed by distinguishing between enantiomers for the first time as a 4D-QSAR approach to reveal the pharmacophore (Pha) and to predict the bioactivity of the dipeptidyl boron compounds. The Electron Conformational Matrices of Congruity (ECMCs) were prepared for all conformers of compounds in the data set based on the quantum chemical calculations at HF/3−21 G level in an aqueous medium. The comparison of the ECMCs within the certain tolerances by the EMRE program revealed the pharmacophore for some dipeptidyl boron derivatives. For the selection of the most influential parameters on the activity and the calculation of theoretical activities, the genetic algorithm with the non-linear least square method was used. The final model was validated by the cross-validation method with the division of the data set into training and test items. The 12-parameter model gave excellent statistical results (R2 training = 0.850, R2 test = 0.809, q2 = 0.755, q2 ext1 = 0.776, q2 ext2 = 0.759, q2 ext3 = 0.735, CCC tr = 0.922, CCC test = 0.846, CCC all = 0.905). Because of the inexistence of 4D-QSAR studies on the dipeptidyl boron derivatives and the stereoisomerism effect on the biological activity was examined for the first time for these compounds, this study plays an important role in the development of new boron-containing compounds. [ABSTRACT FROM AUTHOR]

Gas-phase conformations of the deprotonated disodium cationized 2′-deoxycytidine-5′-monophosphate and cytidine-5′-monophosphate nucleotides, [pdCyd−H+2Na]+ and [pCyd−H+2Na]+, are studied by infrared multiple photon dissociation (IRMPD) action spectroscopy. Analysis of the experimental results is assisted by complimentary electronic structure calculations of low-energy conformers at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory. These calculations provide relative energetics and predicted IR spectra of the calculated conformers for comparison to the measured IRMPD action spectra in the IR fingerprint and hydrogen-stretching regions. Comparisons between the predicted IR and measured IRMPD spectra provide insight into the conformations accessed by [pdCyd−H+2Na]+ and [pCyd−H+2Na]+ during the experiments. Comparison of these calculations and spectroscopic analysis with those performed in previous studies for cytidine nucleotides representing those present in different local environments allows for elucidation of the impact of the local environment on the intrinsic structure of these nucleotides. Comparison of these results with similar studies of the cytidine nucleosides also helps reveal the impact of the phosphate moiety on structure. Although several conformers of both [pdCyd−H+2Na]+ and [pCyd−H+2Na]+ are observed experimentally, a common sodium cation binding mode is observed, highlighting the importance of the stabilization it provides to the cytidine nucleotides. Image 1 • The deprotonated, disodiated forms of pdCyd and pCyd adopt similar conformations. • The phosphate, nucleobase, and sugar are favorable Na+ binding sites of pdCyd and pCyd. • The phosphate moiety of pdCyd and pCyd is the most favorable Na+ binding site. • Chelation interactions are important to sodium cation binding to pdCyd and pCyd. • The local environment strongly influences nucleotide ionization and structure. [ABSTRACT FROM AUTHOR]

• Molecular modeling of synephrine was performed at DFT. • Potential energy scanning was performed with respect to different dihedrals and thus twelve conformers were confirmed. • Vibrational spectra of synephrine molecule in all the conformers were computed. • FTIR and Raman spectra were recorded and correlated with theoretical spectra of most stable conformer of synephrine. • Electronic structure and frontier orbitals energies were also computed. The optimization of isolated synephrine molecule and its HCl cluster was performed. The potential energy scanning with respect to some dihedral angles at ethylamine side chain was also performed which prefers twelve different low energy structures of single synephrine molecule. The effect of N..H hydrogen bond on geometry and vibrational properties of synephrine in the least energy conformer was studied. The vibrational and electronic structures of all the twelve conformers of synephrine were computed. The experimental FTIR and Raman spectra of synephrine were also recorded in the spectral region 4000–400 cm−1 and 3200-50 cm−1 respectively and correlated with the theoretical spectra of energetically most preferred structure of synephrine. The normal coordinate analysis was employed to scale the overestimated DFT frequencies and to calculate potential energy distributions of vibrtional modes of synephrine. The natural bond orbital analysis was also performed to obtain bond energies and occupancies, HOMO-LUMO and hybridization. [ABSTRACT FROM AUTHOR]

• Structures and properties of all possible cyanocyclohexanes were determined by density functional theory. • Dipole moments of greater than 10 d were predicted for some molecules based on the calculations. • Axial substituents exert greater steric demand and contribute more to dipole moments than do equatorial substituents. The effects of position and orientation (axial/equatorial) on the structures and dipole moments of all possible cyano-substituted cyclohexanes were examined using B3LYP/6-311++G**. All optimized molecules exhibited the chair conformation; molecules exhibiting dipole moments ≥6.00 D were examined to determine the effect of substituent position and orientation on the dipole moment. Axial substituents had a greater effect than did equatorial on the dipole moment. For conformer pairs, axial substituents produced higher energy conformers, indicating that equatorial substituents lowered steric interference. Intramolecular non-bonded distances between co-facial axial/axial and vicinal axial/equatorial cyano-groups did not support the idea of greater axial steric demand. The ranges, but not the magnitudes, of ring C-C-C angles were influenced the atoms vicinal to the central carbon atom of the angle. Patterns in the highest occupied and lowest unoccupied molecular orbital energies may provide a basis from which specific cyanocyclohexanes may be "tuned" for electron-acceptor properties. [ABSTRACT FROM AUTHOR]

The effects of the polymeric matrix on the photophysical properties of monomeric dyes reactive to Excited State Intramolecular Proton Transfer (ESIPT) were evaluated by UV–Vis absorption and steady-state and time-resolved emission spectroscopies. A radical polymerization reaction was used to produce new photoactive styrene-based polymeric matrices. The fluorescent polymers had their structural, thermal, electrochemical and photophysical properties evaluated. The benzazole monomers presented excited-state properties dependent on the viscosity induced by the polymeric media, wherein only the ESIPT process extension was unfavoured once the species stability in the excited state did not vary, as observed in the analysis of their fluorescence lifetimes when diluted in organic solvent. Additional experiments performed in the highly viscous non-polar aprotic solvent Nujol, as well as theoretical predictions by the analysis of the energy barriers relative to both the excited state reaction and rotational conformers, performed at the CAM-B3LYP/6–311 + G(d,p) level of theory corroborate these observations. The theoretical calculations showed that the activation energies relative to the conformational balances in the excited state were extremely increased in comparison to those on the ground state, indicating that viscosity is a significant driving force to the ESIPT process. • Effects of the polymeric matrix on the Excited State Intramolecular Proton Transfer (ESIPT) reaction • Excited-state properties dependent on the viscosity induced by the polymeric media • Theoretical calculations showed that viscosity limits the extension of the ESIPT process. [ABSTRACT FROM AUTHOR]

The article presents an analysis of solvent effect on the N-acetyl L-prolyl N-methylamide (AceProNMe) and AceProNMe conformers' population distribution in vacuum as well as in different solvents, suggesting that it is correlated with the solvent's polarity function. Topics addressed include computation of the Boltzman distribution law and the impact of the solvents on the molecular spectra.

Electronic structure, cation-anion binding and spectral characteristics of the alkyl substituted imidazolium dication and Br−, BF 4 −, PF 6 − or CF 3 SO 3 − anion complexes have been obtained employing the M06-2X based density functional theory. The dication-anion complexes serve as model systems for describing dicationic ionic liquids and are facilitated by electrostatic, bifurcated hydrogen bonding (C-H⋯O) and anion---π interactions. The lowest energy conformer possesses relatively strong interactions from reactive vinylic protons on the imidazolium cation whereas the largely destabilized conformers reveal increasing contributions to binding from the interactions arising from by ethyl/butyl substituents at the expense of strong hydrogen bonding from vinylic protons on the imidazolium moiety. Underlying dication-anion binding has been probed through quantum theory of atoms in molecules (QTAIM) approach and the natural bond orbital analyses. It has been predicted that binding energies in the lowest energy complexes of the methyl substituted imidazolium complex emerge with a hierarchy: Br− > BF 4 − > CF 3 SO 3 − > PF 6 −, which is qualitatively different from that of butyl substituted complexes; the latter revealing stronger binding with CF 3 SO 3 − anion. The reactive vinylic proton engenders largely downfield δ H signals (beyond 8.8 ppm) in their 1H NMR spectra. It has been further shown that hydrogen bond energies of the reactive proton (H1) estimated from the QTAIM theory correlate well with the 1H NMR chemical shifts measured from the experiments. The ramifications of dication-anion binding to vibrational spectra are also presented. Unlabelled Image • Binding of alkyl substituted imidazolium (DIm) with different anions is studied. • C1DIm binds strongly to bromide anion than BF 4, CF 3 SO 3 and PF 6 anions. • C4DIm reveals hierarchy toward anion binding: CF 3 SO 3 > Br > BF 4 > PF 6. • NBO and QTAIM analyses employed to probe underlying noncovalent interactions. • δ H of acidic proton from 1H NMR experiment correlates well with the E HB parameter. [ABSTRACT FROM AUTHOR]

• Electronic spectrum of ethanol with complete assignment of all observed electronic features in VUV region is reported for the first time. • Rydberg state assignments of ethanol comprehended with the help of quantum chemical calculations considering the presence of excitations from both trans and gauche conformers of ethanol. • Vibronic features accompanying the 3p Rydberg components are assigned to the fundamental and combination modes of -OH and -CH 3 torsional modes. • The gauche conformer in its ionic limit is predicted to undergo unimolecular dissociation with a large C—C bond length of 1.759 Å. • Potential energy curves envisage that the dissociation of the H atom from ethanol is predominantly from low lying dissociative singlet/triplet state. The electronic spectrum of ethanol (CH 3 CH 2 OH) in the 6–11 eV region is analysed by recording its photoabsorption spectrum using synchrotron radiation source. The electronic spectra comprise predominately weak Rydberg series of ns and np type converging to the first three ionization potentials overriding a broad continuum. DFT calculations on the neutral and ionic ground states of ethanol conformers predicted an unusual large C C bond length for gauch conformers (1.759 Å) at its ionic limit resulting in unimolecular dissociation at 0.28 eV below the ionization potential of trans conformer. Vertical excited state energies computed at TDDFT/CAMPB3LYP level of theory gave an excellent correlation of the experimentally observed spectral features. In the present work the assignment of the observed Rydberg peaks in the VUV region could be adequately interpreted by taking into consideration the presence of excitations from both trans and gauche conformers of ethanol. The n o -3p Rydberg transition and associated vibronic features showed the presence of both conformers in the 7.5–8.5 eV region of electronic spectrum. Plots of the potential energy curve plots of the first few excited states gave insight into the nature of the excited states and confirmed that the lowest state to be dissociative in nature. This is a first report of the comprehensive electronic spectroscopic study of conformers of ethanol in the VUV region. [ABSTRACT FROM AUTHOR]

The discrimination of DNA methylation could make more complicated with the appearance of these minor bases. The conventional bisulfite sequencing faces with the tremendous challenge in the discrimination of DNA methylation. Therefore, the improved and modification bisulfite sequencing has been conducted to raise the reaction selectivity. The key mechanism for these bisulfite sequencing is the reaction of nucleic acids with HSO3− under acidic conditions. The C5═C6 bonds of 5‐methylcytosine (5‐MeCyt) and cytosine (Cyt) have been modified to improve the difference of activation free energies in bisulfite conditions. Because of this, the hydrolytic deamination of DHCytN3+ (paths A and B) and 5‐DHMeCytN3+ isomers (equatorial and axial conformers, paths C and D) has been explored in the presence of the HSO3− group. The activation free energies (ΔGs≠) of DHCytN3+ and 5‐DHMeCytN3+ equatorial conformer paths exhibit no obvious difference, which increases difficulties in differentiating cytosine from 5‐methylcytosine under bisulfite conditions. Meanwhile, the difference of ΔGs≠ between the 5‐DHMeCytN3+ axial conformer and DHCytN3+ is consistent with the experimental results, where the calculated deamination rate is lower for 5,6‐dihydro‐5‐methylcytosine than for 5,6‐dihydrocytosine. And by extrapolation, the differentiating Cyt from 5‐MeCyt may have a greater possibility by bisulfite treatment. These results have high expectations for the experimental scientists to explore new methods to avoid the formation of the 5‐DHMeCytN3+ equatorial conformer. Furthermore, the rate constant with Wigner tunneling correction for paths A, C, and D are in good agreement with uncorrected results. [ABSTRACT FROM AUTHOR]

New 3D conformers were synthesized to show a nanomolecular configuration with geometrically branched 2-diphenylaminofluorene (DPAF-C2M) chromophores using a symmetrical 1,3,5-triaminobenzene ring as the center core for the connection of three fused DPAF-C2M moieties. The design led to a class of cis-cup-tris[(DPAF-C2M)-C60(>DPAF-C9)] 3D conformers with three bisadduct-analogous cages per nanomolecule facing at the same side of the geometrical molecular cis-cup-shape structure. A sequential synthetic route was described to afford this 3D configurated conformer in a high yield with various spectroscopic characterizations. In principle, a nanostructure with a non-coplanar 3D configuration in design should minimize the direct contact or π-stacking of fluorene rings with each other during molecular packing to the formation of fullerosome array. It may also prevent the self-quenching effect of its photoexcited states in solids. Photophysical properties of this cis-cup-conformer were also investigated. [ABSTRACT FROM AUTHOR]

We used a new descriptor called the Klopman index in our software of the "molecular comparative electron topology" (MCET) method to reduce the uncertainty resulting from the descriptors used in QSAR studies. The 3D pharmacophore model (3D-PhaM), which can demonstrate three-dimensional interaction between the ligand -receptor (L-R), is only possible with local reactive descriptors (LRD). The Klopman index, containing both Coulombic and frontier orbital and interactions of atoms of the ligand, is a good LRD. Molecular conformers having the best matching atoms with the template conformer can be selected as one of the most suitable spatial structures for interaction with the receptor, and the LRD values of the atoms in this conformer serve to determine 3D-PhaM. The 3D-PhaM of the N-benzyl benzamide derivatives, such as the melanogenesis inhibitor, was determined by ligand-based MCET and confirmed by the structure-based FlexX docking method. For compounds of the training set (42) and the external cross validation test set (6), the Q2 (0.862) and R2 (0.913) of the statistical parameters were calculated, respectively, and were checked by rm2 (0.85) of the stringent validation. [ABSTRACT FROM AUTHOR]

We have studied the intrinsic fluorescence spectra of a monomeric variant of human transthyretin (M-TTR), a protein involved in the transport of the thyroid hormone and retinol and associated with various forms of amyloidosis, extending our analysis to the second order derivative of the spectra. This procedure allowed to identify three peaks readily assigned to Trp41, as the three peaks were also visible in a mutant lacking the other tryptophan (Trp79) and had similar FRET efficiency values with an acceptor molecule positioned at position 10. The wavelength values of the three peaks and their susceptibility to acrylamide quenching revealed that the three corresponding conformers experience different solvent-exposure, polarity of the environment and flexibility. We could monitor the three peaks individually in urea-unfolding and pH-unfolding curves. This revealed changes in the distribution of the corresponding conformers, indicating conformational changes and alterations of the dynamics of the microenvironment that surrounds the associated tryptophan residue in such transitions, but also native-like conformers of such residues in unfolded states. We also found that the amyloidogenic state adopted by M-TTR at mildly low pH has a structural and dynamical microenvironment surrounding Trp41 indistinguishable from that of the fully folded and soluble state at neutral pH. [ABSTRACT FROM AUTHOR]

Following previous efforts to render the Conformational Space (CS) of flexible compounds by Generative Topographic Mapping (GTM), this polyvalent mapping technique is here adapted to the docking problem. Contact fingerprints (CF) characterize ligands from the perspective of the binding site by monitoring protein atoms that are "touched" by those of the ligand. A "Contact" (CF) map was built by GTM-driven dimensionality reduction of the CF vector space. Alternatively, a "Hybrid" (Hy) map used a composite descriptor of CFs concatenated with ligand fragment descriptors. These maps indirectly represent the active site and integrate the binding information of multiple ligands. The concept is illustrated by a docking study into the ATP-binding site of CDK2, using the S4MPLE program to generate thousands of poses for each ligand. Both maps were challenged to (1) Discriminate native from non-native ligand poses, e.g., create RMSD-landscapes "colored" by the conformer ensemble of ligands of known binding modes in order to highlight "native" map zones (poses with RMSD to PDB structures < 2Å). Then, projection of poses of other ligands on such landscapes might serve to predict those falling in native zones as being well-docked. (2) Distinguish ligands–characterized by their ensemble of conformers–by their potency, e.g., testing the hypotheses whether zones privileged by potent binders are clearly separated from the ones preferred by decoys on the maps. Hybrid maps were better in both challenges and outperformed the classical energy and individual contact satisfaction scores in discriminating ligands by potency. Moreover, the intuitive visualization and analysis of docking CS may, as already mentioned, have several applications–from highlighting of key contacts to monitoring docking calculation convergence. [ABSTRACT FROM AUTHOR]

In this study, three independent methods were used to identify short fragment of both chains of human insulin which are prone for aggregation. In addition, circular dichroism (CD) research was conducted to understand the progress of aggregation over time. The insulin fragments (deca- and pepta-peptides) were obtained by solid-phase synthesis using 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium toluene-4-sulfonate (DMT/NMM/TosO-) as a coupling reagent. Systematic studies allowed identification of the new fragments, expected to be engaged in triggering aggregation of the entire structure of human insulin under physiological conditions. It was found that the aggregation process occurs through various structural conformers and may favor the formation of a fibrous structure of aggregate. [ABSTRACT FROM AUTHOR]

We report a computational study of two series of molecules, one having the Si–O–N linkage and the other with the Si–(CH2)n–N linkage, where n = 1–4. The silicons have various substituents—combinations of H, CH3, F, Cl and CF3. Many of these compounds have been prepared and characterized experimentally. The Si···N distances were found to be relatively short, which may denote a noncovalent interaction or may simply be dictated by the molecular structures. This and the nature of the interaction (if any) were the subjects of our study. We addressed these issues computationally, determining optimized geometries, energies and electrostatic potentials at the density functional M06-2X/6–31 + G(d,p) level. We conclude that there is an attractive Coulombic Si···N interaction in each case, although it is sometimes quite weak. It involves the lone pair of the nitrogen and the positive σ-hole potential produced on the silicon by the bonding from the substituent that is anti to the nitrogen. This accounts for the key features of these molecules, such as the dependence of the Si···N distances upon the electron-withdrawing power of the anti substituent and the effects of gauche chlorines in weakening the interactions. When the Si···N interactions are disrupted by rotation of the N(CH3)2 group or by conversion of the molecules to open-chain conformers, the Si···N distances lengthen and are essentially the same regardless of the substituent in the anti position. These observations confirm the presence of Si···N interactions in the original molecules. [ABSTRACT FROM AUTHOR]

Theoretical studies on the structures, densities, and heats of formation of conformational isomers of 3,4-bis(1H-5-tetrazolyl)furoxan (H2BTF) were performed based on density functional theory (DFT) calculations. Two stable planar conformational isomers, the face-to-back and the back-to-face conformers, and one stable slightly twisted conformer, the back-to-back conformer, were predicted for H2BTF at the M06-2X/6-311 + G(d,p) level of theory. The face-to-back conformer was calculated to be the most stable conformational isomer on the potential energy surface. No stable face-to-face conformer, whether planar or tilted, was identified in the calculations. The Vienna Ab Initio Simulation Package (VASP) was used in combination with molecular dynamics simulation to explore the stable crystal forms and the densities of the stable conformational isomers. Two of them exhibited high densities: the face-to-back conformer with P21 symmetry (2.01 g/cm3) and the back-to-back conformer with Pna21 symmetry (2.05 g/cm3). Their heats of formation were also predicted to be high when calculated at the same DFT level. The detonation pressures and velocities of these polymorphs, as calculated using the EXPLO5 program, are well above those of many advanced high energy density materials, pointing to the potential use of these conformers as novel explosives with good detonation performance. Also, IR spectra are shown to be able to distinguish these denser polymorphs of H2BTF. This study suggests that it could be worth investigating whether denser polymorphs of H2BTF can be grown. [ABSTRACT FROM AUTHOR]

Orion KL is one of the prime templates of astrochemical and prebiotic chemical studies. We wish to explore more organic molecules with increasing complexity in this region. In particular, we have searched for one of the most complex organic molecules detected in space so far, ethyl formate (C2H5OCHO). This species is the next step in chemical complexity after the simplest member of esters (methyl formate, CH3OCHO). The mechanisms leading to its formation are still poorly known. We have used high angular resolution (∼1.″5) ALMA observations covering a large bandwidth from 214 to 247 GHz. We have detected 82 unblended lines of C2H5OCHO (49 and 33 of the trans- and gauche-conformers, respectively). The line images showed that C2H5OCHO arises mainly from the compact ridge and the hot core-southwest regions. The derived rotational temperatures and column densities are 122 ± 34 K, (0.9 ± 0.3) × 1016 cm−2 for the hot core-SW, and 103 ± 13 K, (0.6 ± 0.3) × 1016 cm−2 for the compact ridge. The comparison of spatial distribution and abundance ratios with chemically related molecules (methyl formate, ethanol, and formic acid) indicates that C2H5OCHO is likely formed on the surface of dust grains by addition of CH3 to functional-group radicals (CH2OCHO) derived from methyl formate (CH3OCHO). [ABSTRACT FROM AUTHOR]

Remarkable accomplishments demonstrating the importance of nucleic acids in molecular engineering and computation have been made over the past two decades. However, much of the work in this area so far has been carried out in vitro, utilizing almost exclusively homochiral D-DNAs (or D-RNAs) as chemical building blocks. Such natural building blocks are prone to enzymatic degradation and cross-hybridization with the host's genetic materials. Here we report the development of an orthogonal nucleic acid system that is made up of a left-handed and a right-handed conformer, and a non-helical peptide nucleic acid analogue. We show that the stereochemical information inherent in the right-handed and left-handed conformers can be interconverted from (R) to (S) and vice versa, along with their helical sense and recognition capability, through strand displacement. The genetic information encoded in these synthetic building blocks can be interfaced with DNA or RNA through a molecular converter. Stereo-inverted oligonucleic acids are promising tools for bioengineering but are limited by low availability of suitable monomers. Here the controlled interconversion of helical screw sense in peptide nucleic acid oligomers is achieved through strand displacement. [ABSTRACT FROM AUTHOR]

Through the use of high-level G4-theory calculations, we have investigated the structure, stability, and bonding of a set of Mg derivatives formed by replacing the -OH group of malonaldehyde or only the hydrogen atom of this group by a -MgH group. To give insight into the resonance-assisted phenomenon, which might be involved in the stabilization of these compounds, we also included the corresponding saturated analogs in our survey. The effect of the rigidity of the molecular framework was considered by analyzing the Mg derivatives of (Z)-4-(hydroxymethylene)cyclobut-2-enone, obtained through the same substitutions mentioned above. The effect of replacing the carbonyl group by an imino group was also contemplated. In all cases, the global minimum is a cyclic conformer stabilized through the formation of rather strong intramolecular magnesium bonds. The strength of these interactions is directly related with the intrinsic basicity of the carbonyl group (or the imino group) and the intrinsic acidity of the -MgH group, rather than with a resonance-assisted phenomenon. As a matter of fact, for all the investigated systems, the conclusion is that resonance in the cyclic conformer is directly correlated with the strength of the intramolecular magnesium bond, and not vice versa. Interestingly, the strength and characteristics of these interactions for these Mg-containing derivatives are very similar to those of the corresponding Be-containing analogs. [ABSTRACT FROM AUTHOR]

The relative conformer energies of glycine are evaluated by using a focal point analysis expressed as (). The conformer abundances at various temperatures (298−500 K) are calculated based on the relative energies and Boltzmann statistical thermostatistical analysis with and without considering internal hindered rotations. A comparison between the available Raman spectrum and the electron momentum spectrum confirms that the influence of rigid-rotor hindered rotation on the conformational proportions of glycine is considerable, especially for the IIIp structure. The conformational interconversions are discussed. It is found that with increasing temperature, the mole fraction of IIn keeps constant and Ip structure can convert into IVn and IIIp, leading to the decrease in the weight of Ip and the increase in the weights of IVn and IIIp conformers, which is in accordance with experimental observations. [ABSTRACT FROM AUTHOR]

Summary Relaxases play essential roles in conjugation, the main process by which bacteria exchange genetic material, notably antibiotic resistance genes. They are bifunctional enzymes containing a trans-esterase activity, which is responsible for nicking the DNA strand to be transferred and for covalent attachment to the resulting 5′-phosphate end, and a helicase activity, which is responsible for unwinding the DNA while it is being transported to a recipient cell. Here we show that these two activities are carried out by two conformers that can both load simultaneously on the origin of transfer DNA. We solve the structure of one of these conformers by cryo electron microscopy to near-atomic resolution, elucidating the molecular basis of helicase function by relaxases and revealing insights into the mechanistic events taking place in the cell prior to substrate transport during conjugation. [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]

The author discuss a study by H. P. Reisenauer et al. in the journal "Angewandte Chemie International Edition" that resolves discrepancies in the reported structures of a solid form on carbonic acid (H2CO3). Studies of three different methods for free carbonic acid synthesis, including the irradiation of high-energy mixtures of carbon dioxide (CO2) and water (H2O), and the three conformers of carbonic acid that exist in the gas phase are discussed.

Several tables are presented which shows the bond lengths of benznidazole obtained from X-ray diffraction and density functional theory (DFT) calculated smallest conformer energy in water, bond angles of benznidazole, and dihedral angles of benznidazole.

The article discusses a study regarding the conformational analysis of (R*,S*)-1,1-[methyl(phenyl)phosphoryl]-2-phenyl-1,2λ5-azaphospholane 2-oxide (I). The study used the quantum-chemical calculations and dipole moment method. Results show that conformers IA-ID have zero or near-zero relative energy, but their dipole moments and calculation according to the vector addition scheme did not coincided with I's measurement in benzene.

A theoretical study of elastic electron collisions with 9 conformers of the gas-phase amino acid α-alanine (CH3CH(NH2)COOH) is performed. The eigenphase sums, resonance features, differential and integral cross sections are computed for each individual conformer. Resonance positions for the low-energy shape resonance are found to vary from 2.6 to 3.1 eV and the resonance widths from 0.3 to 0.5 eV. Averaged cross sections for thermal mixtures of the 9 conformers are presented. Both theoretical and experimental population ratios are considered. Thermally averaged cross sections obtained using the best theoretical estimates give reasonable agreement with the observed thermal cross sections. Excited conformers IIA and IIB make a large contribution to this average due to their large permanent dipole moments. [ABSTRACT FROM AUTHOR]

Macrocycles Supramolecular organic frameworks (SOFs) have gathered the attention of the scientific world in recent times due to their fascinating applications in fields, such as selective gas sorption/separation, catalysis, medicinal chemistry, and electronics. In their Communication on page 15202 ff., J. Atwood and co‐workers describe the synthesis and crystal structures of two functionalized resorcin[4]arenes and pyroagllol[4]arenes, SOF building blocks, 4‐hydroxyphenylresorcin[4]arenes, and 4‐hydroxyphenylpyrogallol[4]arenes. [ABSTRACT FROM AUTHOR]

A correction to the article "Transient conformers of LacY are trapped by nanobodies," that was published in the November 10, 2015 issue is presented.

In this paper, gold nanorods (GNRs) were synthesized and characterized by absorption spectroscopy, scanning electronic microscopy and dark-field scattering spectroscopy. The density of nanorods on the glass substrate has been controlled in order to select locations where a single particle can be illuminated by the excitation focal spot. Diarylethene photochromic molecules were deposited on the GNRs and surface enhanced Raman scattering experiments were performed in single particle condition to study both isomer’s forms. In addition, calculations were performed to precisely resolve each isomer’s vibrational modes. By combining both calculation and experiments, the open and closed forms of the photochromic molecule have been characterized. Moreover, the presence of conformers in the case of the open form has been pointed out, which is an important parameter to take into account of the photochromic process due to different photo-activity with respect to the antiparallel or parallel configuration. Thanks to the results obtained, we propose a method that could be used in further experiments to follow photochromic reactions based on the selection of a specific fingerprint, which allows us to unambiguously assign the detected signal to one isomer form of the photochromic molecule. [ABSTRACT FROM AUTHOR]

Carbonyl diazide, (N3)2CO (I), is a highly explosive compound. The isolation of the substance in a neat form was found to provide unique access to two other high-energy molecules, namely, N3-NCO (III) and cycl-N2CO (IV), among the decomposition products of (I). To understand the underlying reaction mechanism, the decomposition reactions including the thermal conversion of two conformers of (I) were revisited, and the potential energy surface (PES) was computationally explored by using the methods of B3LYP/6-311+G(3df) and CBS-QB3. The most stable syn-syn structure (I) readily converts into the syn-anti conformer (ΔH exptl = 1.1 ± 0.5 kcal mol-1), which undergoes decomposition in two competing pathways: a concerted path to N3-NCO (III) or a stepwise route to (III) via the nitrene intermediate N3C(O)N ¹(II). The calculated activation barriers (E a) are almost the same (33 kcal mol-1, B3LYP/6-311+G(3df)). Further decomposition of (III) occurs through a concerted fragmentation into 2 N2 + CO with a moderate E a of 22 kcal mol-1, and this process is compared to the isoelectronic species N3-N3 3 N2 (E a = 17 kcal mol-1) and OCN-NCO N2 + 2 CO (61 kcal mol-1). No low-energy pathway leading to (IV) was found on the singlet PES. However, the intervention of triplet ground-state ³(II) from the initially generated ¹(II) through an intersystem crossing (ISC) offers a likely approach to (IV); that is, ³(II) can decompose in a concerted process (E a = 30 kcal mol-1) by eliminating one N2 to yield the disfavored OCNN ³(VI). A careful intrinsic reaction coordinate analysis and a combined energy scan of the N-C-N angle reveals a bifurcation point on this triplet PES, which allows a spin crossover to the singlet PES along the reaction coordinate and eventually leads to the formation of the metastable diazirinone (IV). [ABSTRACT FROM AUTHOR]

The article discusses a study that investigated the synthesis of m-fluorosulfinylaniline as well as the experimental and theoretical characterization. Topics discussed include the quantum chemical calculations predicting stable conformers which differ by the relative orientation of the fluorine atom and comparison of the spectral data of the title compound with the data obtained by quantum chemical calculations.

Allowing for all combinations of internal single-bond rotamers, 1,296 unique trial structures of γ-Aminobutyric acid (GABA) are obtained. All of these structures are optimized at the M06-2X level of theory and a total of 68 local minimal conformers are found. The nine low-lying conformers are used for further studies. According to the calculated relative Gibbs free energies at M06-2X level of theory, we find that the dispersion is important for the relative energy of GABA. The intramolecular hydrogen bonds and hyperconjugative interaction and their effects on the conformational stability are studied. The results show that both of them have great influence on the conformers. The vertical ionization energies (VIE) are calculated and match the experimental data well. The results show that the neutral GABA in the gas phase is a multi-conformer system and at least four conformations exist. [ABSTRACT FROM AUTHOR]

The claim by Shojaei et al (2011 J. Phys. B: At. Mol. Opt. Phys.44 235101) that the entropy difference between the cis and gauche conformers of 1-butene changes dramatically upon inclusion of hindered-rotor corrections is shown to be incorrect. [ABSTRACT FROM AUTHOR]

Aim. To compare conformational ability of dG and dA and their eight position oxidized nucleosides (8-Oxo-7,8-dihydro-2'-deoxyguanosine, 8oxodG and 2'-deoxy-8-oxo-adenosine, 8oxodA), thus, to answer a biologically important question "Could oxidized bases in comparison with non-modified easier become DNA-like syn-conformations?" Methods. The methods of the quantum-chemical density functional method on the MP2/6-311 + + G (d, p) / / DFP B3LYP/6-31(d, p) theory level in isolated state (ε=1) were used in this work. Results. The complete conformational family of 8oxodG containing 95 conformers with relative Gibbs energy lying in the range of 0-8, 56 kcal / mol and the family of 8oxodA consisting 87 structures with 8.74 kcal / mol under standard conditions were shown for the first time. Comprehensive structural features of conformers and characteristics of intramolecular H-bones stabilizing the conformers are presented. 8oxodG and 8oxodA data were compared with similar data for dG and dA for the first time. Conclusions. Oxidation of dG and dA at the C-8 position triggering their lightweight ability to become syn conformated in comparison with canonical nucleosides was shown for the first time. These results are useful to explain the structural mechanism of mutagenic action at eight position oxidation of purine bases of DNA. [ABSTRACT FROM AUTHOR]