Conformation et spectres de vibration des dérivés halogénés du cyclopentane à basse température

A conformational study by vibrational analysis of cyclopentane and halogenocyclopentanes is performed on the basis of the Raman spectra at a very low temperature and the infrared spectra of these molecules trapped in a rigid matrix.     

Single-molecule pump-probe experiments reveal variations in ultrafast energy redistribution

Single-molecule pump probe (SM2P) is a novel, fluorescence-based technique that allows the study of ultrafast processes on the single-molecule level. Exploiting SM2P we have observed large variations (from 1 ps to below 100 fs) in the energy redistribution times of chemically identical molecules in the same sample. Embedding the molecules in a different matrix or changing the excitation wavelength does not lead to significant changes in the average redistribution time. However, chemically different molecules exhibit different characteristic redistribution times. We therefore conclude that the process measured with the SM2P technique is dominated by intramolecular energy redistribution and not intermolecular transfer to the surrounding matrix. The matrix though is responsible for inducing conformational changes in the molecule, which affect the coupling between electronic and vibrational modes. These conformational changes are the main origin of the observed broad distribution of redistribution times.     

Conformational interconversions in supersonic jets: Matrix IR spectroscopy and model calculations

Terminal conformer populations in supersonic molecular beams have been measured by use of matrix IR spectroscopy. the experimental technique is based on trapping of the beam molecules in to a cryogenic matrix. The ratio of conformational isomers is determined by comparing intensity ratios of infrared absorption bands with those found in analogous experiments with thermal effusive molecular beams. supersonic beams of pure 1,2-difluoroethane a considerable depopulation fo the less stable trans conformer is found, the lowest terminal conformational temperature reached being T_c^t8 = 207 (3) K. In seeded argon beams the cooling of the conformational distribution was found to be weaker. In supersonic beams of 1,2-dichloroethane and of methyl nitrite no significant conformational cooling was found. The experimental results are discussed in terms of a kinetic model of conformational interconversion in the flow field of a continuum free jet. The calculation indicate that conformational cooling by supersonic expansion may be expected only for molecules with a low energy barrier to internal rotation.     

Thermal Effect on Positive Patterned Self-Assembled Monolayer Grown from a Droplet of Alkanethiol

Atomic force microscope technique is widely used for the spatial narrow deposition of molecules inside the bare space of preexisting self-assembled monolayer (SAM) matrix. Using molecular dynamics simulation, we studied the formation of positively patterned SAM from a globule of 1-octadecanethiol (ODT) on predesigned SAM matrix of 1-dodecanethiol (DDT) and effect of temperature on it. The alkyl chains of ODT SAM were densely packed and ordered by means of chemisorption through sulfur atoms. The circular SAM of ODT contained defects due to the molecules those were standing upside down or trapped inside ODT SAM. We found that with the increase of temperature, these defects moved out by flipping of inverted ODT molecules or building spaces to be adsorbed on Au surface. The ODT molecules on the top of the pile of stable circular SAM or those are upside down and trapped disperse in a unique fashion namely serial pushing through which molecules firstly make a free space to enter inside the adsorbed thiol molecules and then push neighboring molecules to get enough space to be adsorbed on the gold surface. The stability of ODT SAM was confirmed by analyzing different structural properties such as tilt angle, tilt orientation. and backbone orientation. We also calculated the diffusion coefficient of the ODT molecules which were on the top of SAM island. © 2019 Wiley Periodicals, Inc.     

ELECT++: Faster conformational search method for docking flexible molecules using molecular similarity

We have developed a program, ELECT++ (Effective LEssening of Conformations by Template molecules in C++), to speed up the conformational search for small flexible molecules using the similar property principle. We apply this principle to molecular shape and, importantly, to molecular flexibility. After molecules in a database are clustered according to flexibility and shape (FCLUST++), additional reagents are generated to screen the conformational space of molecules in each cluster (TEMPLATE++). We call these representative reagents of each cluster template reagents. Template reagents and clustered reagents produce, after reaction, template molecules and clustered molecules, respectively (tREACT++). The conformations of a template molecule are searched in the context of a macromolecular target. Acceptable conformational choices are then applied to all molecules in its cluster, thus effectively biasing conformational space to speed up conformational searches (tSEARCH++). In our incremental search method, it is necessary to calculate the root-mean-square deviations (RMSD) matrix of distances between different conformations of the same molecule to reduce the number of conformations. Instead of calculating the RMSD matrix for all molecules in a cluster, the RMSD matrix of a template molecule is chosen as a reference and applied to all the molecules in its cluster. We demonstrate that FCLUST++ clusters the primary amine reagents from the Available Chemicals Directory (ACD) successfully. The program tSEARCH++ was applied to dihydrofolate reductase with virtual molecules generated by tREACT++ using clustered primary amine reagents. The conformational search by the program tSEARCH++ was about 4.8 times faster than by SEARCH++, with an acceptable range of errors. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1834–1852, 1998     

Motion of star‐branched chains in polymer networks: a Monte Carlo study

A simple model of branched polymers in confined space is developed. Star‐branched polymer molecules are built on a simple cubic lattice with excluded volume and no attractive interactions (good solvent conditions). A single star molecule is trapped in a network of linear polymer chains of restricted mobility. The simulations are carried out using the classical Metropolis algorithm. Static and dynamic properties of the star‐branched polymer are determined using various networks. The dependence of the longest relaxation time and the self‐diffusion coefficient on chain length and network properties are discussed and the proper scaling laws formulated. The possible mechanism of motion is discussed. The differences between the motion of star‐branched polymers in such a network are compared with the cases of a dense matrix of linear chains and regular rod‐like obstacles.     

Cationic agents for DNA compaction

Fluorescence microscopy was used to investigate the conformational changes of individual T4 DNA molecules induced by different compacting agents, namely the cationic surfactants, cetyltrimethylammonium bromide (CTAB) and chloride (CTAC), iron(III), lysozyme, and protamine sulfate. A protocol for establishing size estimates is suggested to obtain reproducible results. Observations show that in the presence of lysozyme and protamine sulfate, DNA molecules exhibit a conformational change from an elongated coil structure to compact globules, usually interpreted as a first-order transition. The maximum degree of compaction that is attained when iron(III) or CTAB (CTAC) are used as compacting agents is considerably smaller, and intermediate structures (less elongated coils) are visible even for high concentrations of these agents. Dynamic light scattering experiments were carried out, for some of the systems, to assess the reliability of size estimates from fluorescence microscopy.     

Effect of polymerized silicic acid on mixed lipid-protein monolayers used as cell-membrane models II. Pepsin-sphingomyelin films

Mixed pepsin-sphingomyelin films exhibit behavior typical of bidimensional systems whose components are miscible in all proportions. The non-polar chains of their components are believed to establish weak hydrophobic interactions. The dynamic compression-expansion II-A curves obtained in the presence of polysilicic acid differ from those recorded in its absence, which may arise from an ionic interaction whereby silicate ions accommodate themselves among the film molecules and bind strongly to the sphingomyelin molecules to form a rigid surface network in which the protein molecules are trapped.     

The conformational statistics of polymer chains as obtained from their energy landscape: a conceptual view of the rotational isomeric state approach

In the rotational isomeric state (RIS) approach the conformational statistics of a polymer chain can be conveniently described in terms of the statistical matrix. In this work it is shown from a conceptual point of view to which degree the projection onto a few states, inherently present in any RIS approach, may lead to systematic deviations for estimation of the a priori probabilities. It is shown that these deviations scale with some power of the inverse temperature. Furthermore an algorithm is presented, deriving the statistical matrix from computer simulations. This algorithm is applied to polyethylene. Comparison with the conformational statistics as obtained from Monte Carlo simulations allows the quality of the statistical matrix elements to be estimated. It turns out that the systematic deviation does not hamper practical applications. Questions like the relevance of the anharmonicity of the energy landscape or consideration of more than nearest-neighbor correlations in the RIS approach are discussed.     

Spiroconjugation in orthothiocarbonates

The He(I) photoelectron (PE) spectra of the orthothiocarbonates 1–3 have been investigated. To understand the splitting pattern in the low energy region a comparison with chemically related molecules has been made. In addition, molecular orbital calculations based on a ZDO model and semiempirical calculations were carried out with variation of dihedral angles. The split of the first four orbitais, which depends very much on the geometry, is explicitly discussed. The splitting due to spiroconjugation amounts to 1.1 eV for 1,0.55 eV for 2, and 0.45 eV for 3.     

Monomer and Excimer Emission in a Conformational and Stacking-Adaptable Molecular System

A design strategy that combines molecular conformation, alkyl chain length, and charge-transfer effects has been developed to obtain conformational and stacking-adaptable donor-acceptor-π type molecules for precisely regulating the monomer and excimer emission in a single luminous platform under different environments. These fluorophores can exhibit bright monomer emissions when they are in the dispersed state based on their planar conformation. However, when the luminous molecules with short alkyl side chains are in the crystalline state, their molecular conformation can become distorted, further inducing strong intermolecular interactions and staggered π-π stacking for bright excimer emission. More importantly, their dispersed and aggregated states can be reversibly regulated in a phase-change fatty acid matrix, to achieve temperature-responsive fluorescence for temperature monitoring and advanced information encryption.     

Nonisomerizable non-retinal chromophores initiate light-induced conformational alterations in bacterioopsin.

The photoactivation of retinal proteins is usually interpreted in terms of C=C photoisomerization of the retinal moiety, which triggers appropriate conformational changes in the protein. In this work several dye molecules, characterized by a completely rigid structure in which no double-bond isomerization is possible, were incorporated into the binding site of bacteriorhodopsin (bR). Using a light-induced chemical reaction of a labeled EPR probe, it was observed that specific conformational alterations in the protein are induced following light absorption by the dye molecules occupying the binding site. The exact nature of these changes and their relationship to those occurring in the bR photocycle are still unclear. Nevertheless, their occurrence proves that C=C or C=NH(+) isomerization is not a prerequisite for protein conformational changes in a retinal protein. More generally, we show that conformational changes, leading to changes in reactivity, may be induced in proteins by optical excitation of simple nonisomerizable dyes located in the macromolecular matrix.     

The conformational preferences of acylphloroglucinols—a promising class of biologically active compounds

Acylphloroglucinols are a broad class of phloroglucinol derivatives characterized by the presence of a COR group, where R is more often an alkyl chain. They are largely present in natural sources and exhibit a variety of biological activities, including antibacterial, antiviral, antifungal, antitumor, antioxidant, and antimalarial. This work reports the results of a systematic conformational study (in vacuo, chloroform, acetonitrile, and water) of a representative number (118) of actual and model acylphloroglucinol structures, considering the most common R chains and investigating conformational preferences and relative energies as well as the influence of specific structural features characterizing significant subsets of compounds. The study aimed at identifying patterns for conformational preferences and at singling out the conformational aspects more closely related to the individuality of different structures, as these are expected to be more closely linked to the differences in the biological activities of different compounds. The results highlight patterns enabling reliable predictions of the conformational preferences of acylphloroglucinol molecules. © 2012 Wiley Periodicals, Inc.     

Combining conformational sampling and selection to identify the binding mode of zinc-bound amyloid peptides with bifunctional molecules

The pathogenesis of Alzheimer's disease (AD) has been suggested to be related with the aggregation of amyloid β (Aβ) peptides. Metal ions (e.g. Cu, Fe, and Zn) are supposed to induce the aggregation of Aβ. Recent development of bifunctional molecules that are capable of interacting with Aβ and chelating biometal ions provides promising therapeutics to AD. However, the molecular mechanism for how Aβ, metal ions, and bifunctional molecules interact with each other is still elusive. In this study, the binding mode of Zn(2+)-bound Aβ with bifunctional molecules was investigated by the combination of conformational sampling of full-length Aβ peptides using replica exchange molecular dynamics simulations (REMD) and conformational selection using molecular docking and classical MD simulations. We demonstrate that Zn(2+)-bound Aβ((1-40)) and Aβ((1-42)) exhibit different conformational ensemble. Both Aβ peptides can adopt various conformations to recognize typical bifunctional molecules with different binding affinities. The bifunctional molecules exhibit their dual functions by first preferentially interfering with hydrophobic residues 17-21 and/or 30-35 of Zn(2+)-bound Aβ. Additional interactions with residues surrounding Zn(2+) could possibly disrupt interactions between Zn(2+) and Aβ, which then facilitate these small molecules to chelate Zn(2+). The binding free energy calculations further demonstrate that the association of Aβ with bifunctional molecules is driven by enthalpy. Our results provide a feasible approach to understand the recognition mechanism of disordered proteins with small molecules, which could be helpful to the design of novel AD drugs.     

Density functional calculations of potential energy surface and charge transfer integrals in molecular triphenylene derivative HAT6

We investigate the effect of structural fluctuations on charge transfer integrals, overlap integrals, and site energies in a system of two stacked molecular 2,3,6,7,10,11-hexakishexyloxytriphenylene (HAT₆), which is a model system for conducting devices in organic photocell applications. A density functional based computational study is reported. Accurate potential energy surface calculations are carried out using an improved meta-hybrid density functional to determine the most stable configuration of the two weakly bound HAT₆ molecules. The equilibrium parameters in terms of the twist angle and co-facial separation are calculated. Adopting the fragment approach within the Kohn–Sham density functional framework, these parameters are combined to a lateral slide, to mimic structural/conformational fluctuations and variations in the columnar phase. The charge transfer and spatial overlap integrals, and site energies, which form the matrix element of the Kohn–Sham Hamiltonian are derived. It is found that these quantities are strongly affected by the conformational variations. The spatial overlap between stacked molecules is found to be of considerable importance since charge transfer integrals obtained using the fragment approach differ significantly from those using the dimer approach.     

Fluorescent porphyrins trapped in monolithic SiO2 gels

Macrocyclic molecules play key roles in basic processes in living organisms. Free bases and the metal complexes of porphyrins exhibit a wide range of important optical properties. In these systems the position of the most intense absorption band depends on the peripheral substituents of the macrocycle. Sol-gel methods have generally allowed the successful trapping of porphyrins into inorganic networks. The materials obtained are strong and transparent monolithic gels, but in the majority of cases the red fluorescence of the porphyrins disappears with ageing. We have evaluated the effect of the type and spatial disposition of the substituents in the porphyrin macrocycle periphery on key optical properties, with particular emphasis on the conservation of red fluorescence when porphyrins are simply trapped or covalently bonded to the inorganic matrix. Here, we report the use of the sol-gel procedures to obtain monolithic gels with the hydroxyl- or amino-substituted α, β, γ, δ-tetraphenylporphyrins, (H₂T(S)PP), simply trapped or covalently bonded to the SiO₂ matrix.     

Site-specific Heterogeneity of Multi-domain Human Serum Albumin and its Origin: A Red Edge Excitation Shift Study†

Conformational heterogeneity is a defining characteristic of a protein and is vital in understanding its function and folding landscape. In the present work, we interrogated the presence of conformational heterogeneity in multi-domain human serum albumin in a domain-specific manner using red edge excitation shift (REES) in its native state and also monitored its variation along the unfolding transition. We also looked into the origin of such conformational heterogeneity by varying the solution viscosity. We observed (1) even in the native state, the heterogeneity and dynamics of the side chain exhibit varied behaviors depending on which domain of the multi-domain human serum albumin (HSA) is being examined. (2) When the protein is in the unfolded state, the extent of REES is rendered unimportant since there is a greater quantity of free water present, in addition to the disruption of the protein's structure. (3) While the rigid protein matrix provides the rigidity of domain-I and domain-III, the rigidity of domain-II is provided by water molecules, which indicates that the role of water molecules in providing the rigidity is significant. Overall, our results provide direct evidence of the rigidity and alternate side chain packing arrangement of protein core that varies domain-wise in multi-domain HSA.     

A method for correlations analysis of coordinates: applications for molecular conformations

We describe a new method to analyze multiple correlations between subsets of coordinates that represent a sample. The correlation is established only between specific regions of interest at the coordinates. First, the region(s) of interest are selected at each molecular coordinate. Next, a correlation matrix is constructed for the selected regions. The matrix is subject to further analysis, illuminating the multidimensional structural characteristics that exist in the conformational space. The method's abilities are demonstrated in several examples: it is used to analyze the conformational space of complex molecules, it is successfully applied to compare related conformational spaces, and it is used to analyze a diverse set of protein folding trajectories.     

The interaction of formohydroxamic acid with carbon monoxide: FTIR matrix isolation and quantum chemistry studies

Argon matrix infrared spectra of the complexes formed between formohydroxamic acid (HCONHOH) and carbon monoxide have been recorded. The experimental results indicate formation of three isomeric complexes. In two complexes the NH or OH groups of formohydroxamic acid are attached to the carbon atom of the CO molecule and in the third complex the NH group interacts with the oxygen atom of CO. The formohydroxamic acid complex with two CO molecules is also trapped in the matrix. One of the two CO molecules interacts with the NH group and the second one with the OH group of HCONHOH, in both cases the site of interaction is the carbon atom of CO. Theoretical studies of the structure and spectral characteristics of the complexes were carried out on the DFT(B3LYP)/6-311++G(2d,2p) level. The calculated vibrational frequencies for the complexes present in the matrices are in good agreement with the experimental data. The calculations show also an additional potential energy minimum corresponding to the complex in which the OH group of formohydroxamic acid is attached to the oxygen atom of carbon monoxide.