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     

Shapes of sulfur, oxygen, and nitrogen mustards

Thorough conformational analyses have been performed on representative sulfur, oxygen, and nitrogen mustards. A total of 23, 18, and 38 unique conformers have been located for SM, OM, and NM, respectively, at the MP2/aug-cc-pVDZ level of theory. Despite the fact that these molecules differ only in the identity of the central heteroatom, comparison of their low energy conformations reveals that the shapes they adopt are distinctive to each molecule. Potential energy surfaces for CH(2)-X (X = S, O, and N-CH(3)) and CH(2)-CH(2) bond rotations are presented and, where possible, compared with dihedral angle distributions observed in crystal structure data. These results were used to benchmark and improve the performance of the MM3 and MMFF94 force fields.     

Redistribution of emitting state population in conjugated polymers probed by single-molecule fluorescence polarization spectroscopy

Fluctuations in the fluorescence polarization degree and direction are reported for the first time for single conjugated polymer molecules embedded in a polystyrene matrix at room temperature. The polymer molecule, a polythiophene derivative, clearly emits as a multi-chromophore ensemble showing that the energy does not funnel to any specific low-energy trap. The fluorescence instead originates from thermally populated exciton states with different relative orientations of the transition dipole moments. The fluctuations in the fluorescence polarization are explained in terms of changes in the relative contributions of the different exciton states to the signal due to conformational fluctuations of the molecule or selective exciton quenching by triplet states.     

New Tools for Investigating Electromagnetic Hot Spots in Single‐Molecule Surface‐Enhanced Raman Scattering

Surface‐enhanced Raman scattering (SERS) is quickly growing as an analytical technique, because it offers both molecular specificity and excellent sensitivity. For select substrates, SERS can even be observed from single molecules, which is the ultimate limit of detection. This review describes recent developments in the field of single‐molecule SERS (SM‐SERS) with a focus on new tools for characterizing SM‐SERS‐active substrates and how they interact with single molecules on their surface. In particular, techniques that combine optical spectroscopy and microscopy with electron microscopy are described, including correlated optical and transmission electron microscopy, correlated super‐resolution imaging and scanning electron microscopy, and correlated optical microscopy and electron energy loss spectroscopy.     

Direct Time‐Domain Observation of Conformational Relaxation in Gas‐Phase Cold Collisions

Cooling molecules in the gas phase is important for precision spectroscopy, cold molecule physics, and physical chemistry. Measurements of conformational relaxation cross sections shed important light on potential energy surfaces and energy flow within a molecule. However, gas‐phase conformational cooling has not been previously observed directly. In this work, we directly observe conformational dynamics of 1,2‐propanediol in cold (6 K) collisions with atomic helium using microwave spectroscopy and buffer‐gas cooling. Precise knowledge and control of the collisional environment in the buffer‐gas allows us to measure the absolute collision cross‐section for conformational relaxation. Several conformers of 1,2‐propanediol are investigated and found to have relaxation cross‐sections with He ranging from σ=4.7(3.0)×10^?18 cm² to σ>5×10^?16 cm². Our method is applicable to a broad class of molecules and could be used to provide information about the potential energy surfaces of previously uninvestigated molecules.     

Molecular modelling of liquid crystal systems: An internal coordinate Monte Carlo approach

A Monte Carlo scheme is presented which is designed to provide a convenient mechanism to model accurately the internal molecular structure of liquid crystalline molecules. The technique stores atomic positions in terms of bond lengths, bond angles and dihedral angles within a Z-matrix, and the Monte Carlo scheme involves generating trial configurations from changes to the Z-matrix using the MM2 molecular mechanics potential to describe energy changes between different molecular conformations. The technique is applied to the liquid crystal molecule 4-n-pentyl-4'-cyanobiphenyl (5CB), and results are presented for the conformational populations and dihedral angle distributions of 5CB in the gas phase at 300 K. The effect of a nematic mean field on the distribution of molecular conformations is also examined via the addition of a conformation-dependent potential of mean torque to the internal energy.     

Calculating zeros: Non-equilibrium free energy calculations

Free energy calculations on three model processes with theoretically known free energy changes have been performed using short simulation times. A comparison between equilibrium (thermodynamic integration) and non-equilibrium (fast growth) methods has been made in order to assess the accuracy and precision of these methods. The three processes have been chosen to represent processes often observed in biomolecular free energy calculations. They involve a redistribution of charges, the creation and annihilation of neutral particles and conformational changes. At very short overall simulation times, the thermodynamic integration approach using discrete steps is most accurate. More importantly, reasonable accuracy can be obtained using this method which seems independent of the overall simulation time. In cases where slow conformational changes play a role, fast growth simulations might have an advantage over discrete thermodynamic integration where sufficient sampling needs to be obtained at every λ-point, but only if the initial conformations do properly represent an equilibrium ensemble. From these three test cases practical lessons can be learned that will be applicable to biomolecular free energy calculations.     

Matrix Isolation‐Vibrational Circular Dichroism Spectroscopy of 3‐Butyn‐2‐ol and its Binary Aggregates

Vibrational circular dichroism (VCD) spectroscopy has a unique specificity to chirality and is highly sensitive to the conformational equilibria of chiral molecules. On the other hand, the matrix‐isolation (MI) technique allows substantial control over sample compositions, such as the sample(s)/matrix ratio and the ratio among different samples, and yields spectra with very narrow bandwidths. We combined VCD spectroscopy with the MI technique to record MI‐VCD and MI‐vibrational absorption spectra of 3‐butyn‐2‐ol at different MI temperatures, which allowed us to investigate the conformational distributions of its monomeric and binary species. Good mirror‐imaged MI‐VCD spectra of opposite enantiomers were achieved. The related conformational searches were performed for the monomer and the binary aggregate and their vibrational absorption and VCD spectra were simulated. The well‐resolved experimental MI‐VCD bands provide the essential mean to assign the associated vibrational absorption spectral features correctly to a particular conformation in case of closely spaced bands. By varying the matrix temperature, we show that one can follow the self‐aggregation process of 3‐butyn‐2‐ol and confidently correlate the MI‐VCD spectral features with those obtained for a 0.1 M CCl₄ solution and as a neat liquid at room temperature. Comparison of the aforementioned experimental VCD spectra shows conclusively that there is a substantial contribution from the 3‐butyn‐2‐ol aggregate even at 0.1 M concentration. This spectroscopic combination will be powerful for studying self‐aggregation of chiral molecules, and chirality transfer from a chiral molecule to an interacting achiral molecule and in electron donor–acceptor chiral complexes.     

Conformational elasticity theory of chain molecules

This paper develops a conformational elasticity theory of chain molecules, which is based on three key points: (i) the molecular model is the rotational isomeric state (RIS) model; (ii) the conformational distribution function of a chain molecule is described by a function of two variables, the end-to-end distance of a chain conformation and the energy of the conformation; (iii) the rule of changes in the chain conformational states during deformation is that a number of chain conformations would vanish. The ideal deformation behavior calculated by the theory shows that the change in chain conformations is physically able to make the upward curvature of the stress-strain curve at the large-scale deformation of natural rubber. With the theory, different deformation behaviors between polymers with different chemical structures can be described, the energy term of the stress in the deformations can be predicted, and for natural rubber the fraction of the energy term is around 13%, coinciding with the experi     

Torsional flexing: Conformational searching of cyclic molecules in biased internal coordinate space

A new stochastic (Monte Carlo) procedure, termed torsional flexing, has been devised for searching the conformational space of cyclic molecules. Torsional flexing causes a local, torsion angle-biased, distortion of a ring bond in a cyclic molecule. Because torsional flexing does not cause large atomic movements, even when it is applied to several bonds simultaneously, subsequent energy minimization generally proceeds rapidly. Nevertheless, the torsional flexing method is prone to generate structures that cross energy barriers so that the structure resulting after energy minimization is frequently a different conformer of the cyclic molecule. Conformational searches on cycloheptadecane, oxobrefeldin A, cyclopenta-L -alanine, and rifamycin SV based upon torsional flexing indicated that torsional flexing is among the best methods yet devised for searching the conformational space of flexible cyclic molecules. © 1993 John Wiley & Sons, Inc.     

Identification of conformational structures of 2-phenylethanol and its singly hydrated complex by mass selective high-resolution spectroscopy and ab initio calculations

The flexible prototype molecule 2-phenylethanol (2-PE) and its singly hydrated complex have been investigated in a cold supersonic beam by a combination of high-resolution two-color R2PI spectroscopy and quantum chemistry ab initio calculations. The existence of two monomer structures separated by a high potential energy barrier, gauche and anti ones, was proven. Higher energy conformers are supposed to relax to the observed ones during the jet expansion process. We have identified the conformational structure of the complex between 2-PE and water, which corresponds to water binding to the most stable gauche conformer. No detectable structural changes of the host 2-PE molecule have been observed upon attachment of a single water molecule. A conformational relaxation mechanism is suggested also for the 2-PE x H2O complex.     

Matrix isolation vibrational spectroscopy as a tool for studying conformational isomerism

The use of matrix isolation vibrational spectroscopy to study conformational isomerism is described. Methods of distinguishing conformational splitting from matrix splitting are discussed. Examples are given of molecules for which the conformational equilibrium existing in the gas phase prior to deposition is trapped out in the matrix, of molecules which exhibit reversible interconversion of conformers at matrix temperatures, and of a molecule for which the conformational distribution trapped out in the matrix is strongly dependent on matrix polarity. Results obtained for molecules which exhibit infrared-induced isomerisation in matrices are discussed.     

The electrostatic probe: a tool for the investigation of the Aβ(1-16) peptide deformations using the static modes

We investigate the conformational changes of the Amyloid β(1-16) peptide induced by moving Zn(2+) ions in the solvent, which we call the electrostatic probe. We use our recently developed approach of static modes which allows treating the flexibility of biological molecules at the atomic scale. Starting from an experimental apostructure, we find that several ion impacts allow the transition of the peptide toward its folded conformation, observed experimentally in the presence of Zn(2+) ions. This result shows the ability of our model and its associated software tool to describe properly the conformational changes and opens a new path toward the molecule/molecule docking problem.     

Monitoring the electrochemistry of single molecules by surface-enhanced Raman spectroscopy

Coherent control of chemical species in complex systems is always subject to intrinsic inhomogeneities from the environment. For example, slight chemical modifications can decisively affect transport properties of molecules on surfaces. Hence, single-molecule (SM) studies are the best solution to avoid these problems and to study diverse phenomena in biology, physics, and chemistry. Along these lines, monitoring SM redox processes has always been a "holy grail" in electrochemistry. To date, claims of SM electrochemistry by spectroscopy have come only from fluorescence quenching of polymers and redox-fluorescent molecules. In unconnected developments, the potential of the bianalyte surface-enhanced Raman scattering (SERS) method as a technique with SM sensitivity has been demonstrated. Raman spectroscopy has the potential to explore SM detection of any molecule, independent of its chemical nature. We provide definitive proof of SM events following redox cycles using SERS. The superior sensitivity and spectral richness of SERS makes it general enough to study, in principle, SM electron transfer of any (label-free) molecule.     

Computational analysis of native and modified oligofructosides

This paper presents a quantum chemical calculation of native (2–7 fructoside residues) and chemically modified (2–4 fructoside residues) levan molecule models. A levan modification was carried out by oxidation and the following reduction or hyrdazonation of the fructoside rings. The conformational particularity and reaction ability was studied for the native and for the modified levan molecules.     

Negative thermal expansion of poly(vinylidene fluoride) and polyethylene tie molecules: A molecular dynamics study

The mechanism of thermal actuation for poly(vinylidene fluoride) (PVDF) and polyethylene (PE) tie molecules has been investigated using molecular dynamics simulations. Tie molecules are found in semicrystalline polymers and are polymer chains that link two (or more) crystalline lamellae, allowing for the transfer of force between these regions. A novel simulation technique has been developed to enable measurement of changes in the tie molecule length upon heating. We investigate the dependence of the percentage actuation observed upon heating, on the external applied force that stretches the tie molecules, the temperature range used for heating as well as the length and the number of tie molecules. Two molecular level mechanisms for actuation are identified. An entropically driven mechanism occurs at low applied forces and is applicable to all flexible polymers. A second mechanism due to conformational changes is observed for PVDF but not for PE at intermediate applied forces. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 2223–2232     

An exploration of a novel strategy for superposing several flexible molecules

Summary This paper describes a computational strategy for the superposition of a set of flexible molecules. The combinatorial problems of searching conformational space and molecular matching are reduced drastically by the combined use of simulated annealing methods and cluster analysis. For each molecule, the global minimum of the conformational energy is determined by annealing and the search trajectory is retained in a history file. All the significantly different low-energy conformations are extracted by cluster analysis of data in the history file. Each pair of molecules, in each of their significantly different conformations, is then matched by simulated annealing, using the difference-distance matrix as the objective function. A set of match statistics is then obtained, from which the best match taken from all different conformations can be found. The molecules are then superposed either by reference to a base molecule or by a consensus method. This strategy ensures that as wide a range of conformations as possible is considered, but at the same time that the smallest number of significantly different conformations is used. The method has been tested on a set of six angiotensin II antagonists with between 7–11 rotatable bonds.     

Empirical methods for computing molecular partition coefficients: II. Inclusion of conformational flexibility within fragment–based approaches

A novel algorithm for computing the water/1-octanol partition coefficient, log P , of conformationally flexible molecules, has been investigated using calculations upon a number of uncharged, linear dipeptides. In this method (which appears to be the first to consider explicitly the effects of the population of accessible conformational minima in both phases), the partition coefficient for each dipeptide was calculated from the overall energy change associated with moving the relevant gas-phase conformational distribution into water and into 1-octanol. These energies were computed using solvation contributions based upon the solvent accessible molecular surface area and two sets of empirical parameters. In these initial studies, gas-phase conformational minima were generated using systematic search methods. While the standard error in the computed log P values was disappointing, reasonable agreement was observed between calculated and experimental log P values for the set of model dipeptides, especially when specific hydration interactions involving polar fragments were correctly included in the empirical solvation term. These results indicate that the physical basis of many correction factors employed in the ClogP algorithm for computing log P probably arise from neglect of the redistribution of conformer populations as flexible molecules partition between water and 1-octanol.