Rapid and efficient microwave-assisted synthesis of highly sulfated organic scaffolds

Sulfation of multiple hydroxylated small organic molecules is fraught with problems of poor yield, multitude of products, and long reaction times. We have developed a rapid microwave-based method for synthesis of highly sulfated small organic molecules, which affords the per-sulfated product in moderate to excellent yields and high purity. The method is expected to be of value in the discovery of per-sulfated organic molecules as mimics of glycosaminoglycans, which are being increasingly recognized as modulators of key physiological functions.     

Energy Surface and Conformation Dynamics of Molecules

The topology of energy surfaces and the dynamics of conformationally-labile molecules are discussed. A base model is introduced for an ideal lattice on a multidimensional torus for the energy level surfaces of rotational-isomeric chains. Specific features of the dynamics of molecules of various types are discussed, together with the problems of the formation of a three-dimensional structure and the link between the conformational mobility and the chemical act of reactions.     

Many-centered and one-centered plethysms in the problem of many centers

The concept of a “multi-centered plethysm” for multinuclear problems is defined and studied. Schemes of links of atoms in molecules or complexes and corresponding schemes of the group reductions are considered.     

Revisiting the calculation of condensed Fukui functions using the quantum theory of atoms in molecules

The analysis of previously reported shortcomings of the condensed Fukui functions obtained making use of the quantum theory of atoms in molecules indicates these drawbacks are due to the inadequacy of the definition employed to compute them and not to the partitioning. A new procedure, which respects the mathematical definition and solves these problems, is presented for the calculation of condensed Fukui functions for atomic basins defined according to the quantum theory of atoms in molecules. It is tested in a set of 18 molecules, which includes the most controversial reported cases.     

Synthetic Molecules that Protect Cells from Anoikis and Their Use in Cell Transplantation

One of the major problems encountered in cell transplantation is the low level of survival of transplanted cells due to detachment‐induced apoptosis, called anoikis. The present study reports on the chemical synthesis and biological evaluation of water‐soluble molecules that protect suspended cells from anoikis. The synthetic molecules bind to and induce clusters of integrins and heparan‐sulfate‐bound syndecans, two classes of receptors that are important for extracellular matrix‐mediated cell survival. Molecular biological analysis indicates that such molecules prolong the survival of suspended NIH3T3 cells, at least in part, by promoting clustering of syndecan‐4 and integrin β1 on the cell surface, leading to the activation of small GTPase Rac‐1 and Akt. In vivo experiments using animal disease models demonstrated the ability of the molecules to improve cell engraftment. The cluster‐inducing molecules may provide a starting point for the design of new synthetic tools for cell‐based therapy.     

Field Desorption Mass Spectrometry

Field desorption (FD) enables mass-spectrometric investigation of large organic molecules without their vaporization. The present state of our theoretical understanding of the ionization of these molecules in the adsorbed state on organic emitters is described. The special problems of the technique and prospective developments in the apparatus for future analytical problems are outlined. The present progress report concentrates on analytical studies of biochemical model compounds and degradation products from environmental chemicals and drugs. The method is particularly suitable for the detection and identification of submicrogram quantities of underivatized polar substances present in complex mixtures or pre-purified extracts from biological materials.     

Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions

A recently proposed molecular dynamics method for estimating binding free energies is applied to the complexation of two charged benzamidine inhibitors with trypsin. The difficulties with calculations of absolute binding energies for charged molecules, associated with long-range electrostatic contributions, are discussed and it is shown how to deal with these effectively. In particular, energetic effects caused by the trunction of dipole-dipole interactions in the medium surrounding the charged ligand are examined and found to be significant. Calculations of the absolute binding energy for benzamidine using the free energy perturbation approach are also reported. These simulations illustrate the typical problems associated with annihilation transformations of molecules bound inside proteins. © 1996 by John Wiley & Sons, Inc.     

Computer processing and interpretation of mass spectral information. VIII—ariadna system

The structure of a laboratory system for processing and interpreting mass spectral data intended to solve a wide range of analytical problems (determination of the composition and structure of molecules, isotopic analysis, etc) and research problems (study of the structure and reactivity of ions in the gas phase) is described and its functional possibilities are discussed. The basic software of the system includes both methods for calculation of elemental compositions of ions with the use of masses and amplitudes of isotopic peaks and methods for establishing spectralstructural correlations based on information theory and molecular graph theory.     

One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological properties

Many chemoinformatics applications, including high-throughput virtual screening, benefit from being able to rapidly predict the physical, chemical, and biological properties of small molecules to screen large repositories and identify suitable candidates. When training sets are available, machine learning methods provide an effective alternative to ab initio methods for these predictions. Here, we leverage rich molecular representations including 1D SMILES strings, 2D graphs of bonds, and 3D coordinates to derive efficient machine learning kernels to address regression problems. We further expand the library of available spectral kernels for small molecules developed for classification problems to include 2.5D surface and 3D kernels using Delaunay tetrahedrization and other techniques from computational geometry, 3D pharmacophore kernels, and 3.5D or 4D kernels capable of taking into account multiple molecular configurations, such as conformers. The kernels are comprehensively tested using cross-validation and redundancy-reduction methods on regression problems using several available data sets to predict boiling points, melting points, aqueous solubility, octanol/water partition coefficients, and biological activity with state-of-the art results. When sufficient training data are available, 2D spectral kernels in general tend to yield the best and most robust results, better than state-of-the art. On data sets containing thousands of molecules, the kernels achieve a squared correlation coefficient of 0.91 for aqueous solubility prediction and 0.94 for octanol/water partition coefficient prediction. Averaging over conformations improves the performance of kernels based on the three-dimensional structure of molecules, especially on challenging data sets. Kernel predictors for aqueous solubility (kSOL), LogP (kLOGP), and melting point (kMELT) are available over the Web through: http://cdb.ics.uci.edu.     

New Applications of Computers in Chemistry

The mathematical model of constitutional chemistry described here is based on a concept of isomerism which has been extended from molecules to ensembles of molecules. A chemical reaction is the conversion of an ensemble of molecules into an isomeric ensemble. An ensemble of molecules is representable by an atomic vector and an associated bond and electron (BE)- matrix, and a reaction by a reaction (R)-matrix. These BE-and R-matrices serve as a basis for computer programs for the deductive solution of chemical problems. We present here algorithms and computer programs based on the theory of BE- and R-matrices. They enable the classification and documentation of structrues, substructures and reactions, the prognosis of reaction products,the design of syntheses, the construction of networks of mechanistic and synthetic pathways and the prediction of chemical reactions.     

Identification of the cellular targets of bioactive small organic molecules using affinity reagents

The elucidation of molecular targets of bioactive small organic molecules remains a significant challenge in modern biomedical research and drug discovery. This tutorial review summarizes strategies for the derivatization of bioactive small molecules and their use as affinity probes to identify cellular binding partners. Special emphasis is placed on logistical concerns as well as common problems encountered during such target identification experiments. The roadmap provided is a guide through the process of affinity probe selection, target identification, and downstream target validation.     

Orbital-optimized opposite-spin scaled second-order correlation: an economical method to improve the description of open-shell molecules

Coupled-cluster methods based on Brueckner orbitals are well known to resolve the problems of symmetry breaking and spin contamination that are often associated with Hartree-Fock orbitals. However, their computational cost is large enough to prevent application to large molecules. Here the authors present a simple approximation where the orbitals are optimized with the mean-field energy plus a correlation energy taken as the opposite-spin component of the second-order many-body correlation energy, scaled by an empirically chosen parameter (recommended as 1.2 for general applications). This "optimized second-order opposite-spin" (abbreviated as O2) method requires fourth-order computation on each orbital iteration. O2 is shown to yield predictions of structure and frequencies for closed-shell molecules that are very similar to scaled second-order Moller-Plesset methods. However, it yields substantial improvements for open-shell molecules, where problems with spin contamination and symmetry breaking are shown to be greatly reduced.     

Evaluation of molecule-microbe interactions with capillary electrophoresis: procedures, utility and restrictions

Understanding the interactions between molecules and living organisms is of paramount importance for the evaluation of pharmaceutical activity, chemical toxicity and all manner of microbiological studies. The capability of capillary electrophoresis (CE) in the evaluation of molecule-microbe interactions is examined in the present paper. The fundamental chemical concept of the binding or association constant for molecular systems measured in free solution is discussed for biological systems where microorganisms uptake or associate with molecules from their environment. The heterogeneity of the living organisms must be understood and accounted for including differences related to semantics such as concentration units and the nature of the associations between two entities and large differences in the size and number of microorganisms as compared to molecules. Finally, the added complexity and even inhomogeneity of a cell compared to most molecular systems must be considered and possibly controlled. The binding of specific molecules to viruses is discussed. CE can be utilized to quickly determine if a molecule binds very strongly or not at all to a cell (i.e., a binary yes/no answer). This could be useful for initial high-throughput screening purposes when using capillary arrays, for example. CE can be useful for determining unusual (large) molecule/microbe stoichiometries. Finally, CE can sometimes be used to determine the size of binding constants (K(RL)) within certain limits provided experimental conditions can be formulated that minimize problems of biological heterogeneity.     

A general and efficient Monte Carlo method for sampling intramolecular degrees of freedom of branched and cyclic molecules

A simple and easily implemented Monte Carlo algorithm is described which enables configurational-bias sampling of molecules containing branch points and rings with endocyclic and exocyclic atoms. The method overcomes well-known problems associated with sequential configurational-bias sampling methods. A "reservoir" or "library" of fragments are generated with known probability distributions dependent on stiff intramolecular degrees of freedom. Configurational-bias moves assemble the fragments into whole molecules using the energy associated with the remaining degrees of freedom. The methods for generating the fragments are validated on models of propane, isobutane, neopentane, cyclohexane, and methylcyclohexane. It is shown how the sampling method is implemented in the Gibbs ensemble, and validation studies are performed in which the liquid coexistence curves of propane, isobutane, and 2,2-dimethylhexane are computed and shown to agree with accepted values. The method is general and can be used to sample conformational space for molecules of arbitrary complexity in both open and closed statistical mechanical ensembles.     

Regenerative chemical biology: current challenges and future potential

The enthusiasm surrounding the clinical potential of embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) is tempered by the fact that key issues regarding their safety, efficacy, and long-term benefits have thus far been suboptimal. Small molecules can potentially relieve these problems at major junctions of stem cell biology and regenerative therapy. In this review we will introduce recent advances in these important areas and the first generation of small molecules used in the regenerative context. Current chemical biology studies will provide the archetype for future interdisciplinary collaborations and improve clinical benefits of cell-based therapies.     

Standardless spectrochemical analysis and direct simulations of time-resolved vibronic spectra of polyatomic molecules, isomers and mixtures

The efficient method for calculation of dynamical time-resolved vibronic spectra of polyatomic molecules is proposed. It allows to perform direct real-time computer simulations of such spectra for models of complex compounds, isomers and multicomponent mixtures with quantum beats and non-radiative vibrational relaxation taken into account. The examples of calculated spectra show the ways of how to search and select optimal experimental conditions and retrieve the most informative data for solution of inverse spectral problems in different situations. The new method of standardless analysis based on time-resolved vibronic spectroscopy has been developed and its main ideas are presented here. This method is able to solve quantitative and qualitative spectrochemical problems for individual substances and multicomponent mixtures (even for species with similar optical properties) with the use of experimentally measured relative intensities of dynamical spectra only. The algorithms of how to perform analysis in various experimental conditions are proposed.     

New insights on the stereodynamics of ethylene adsorption on an oxygen-precovered silver surface

The control of spatial orientation of molecules has a great influence on the stereodynamics of elementary processes occurring both in homogeneous and heterogeneous phases. Nonpolar molecules have so far escaped direct experimental investigations because of their poor sensitivity to several external constraints. Recently, it has been shown that the collisional alignment produced in supersonic expansions coupled with molecular-beam velocity selection can help solve such problems. Here we show that the sticking probability of ethylene, a nonpolar molecule prototypical of unsaturated hydrocarbons, on an O(2)-precovered Ag(001) surface is larger for molecules approaching in a helicopter-like motion than for those cartwheeling. A mechanism involving a weakly bound precursor state is suggested, with helicopter molecules having a lower chance of being scattered back into the gas phase than cartwheels when colliding with preadsorbed ethylene.     

The half-projected Hartree-Fock method

A SCF method based on the solution of two eigenvalue problems, in the same manner as for the normal UHF procedure, is formulated for determining the half-projected Hartree-Fock (HPHF) function for singlet ground states of molecules, the HPHF function being defined as a linear combination of two Slater determinants containing only spin eigenfunctions with even quantum number. A computer program has been written and is described, and results are presented for two simple linear molecules. An important part of the correlation energy is obtained for these molecules.