Understanding molecular structure from molecular mechanics

Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.     

Polyvalent carbocyanine molecular beacons for molecular recognitions

Polyvalent carboxylate-terminating near-infrared (NIR) carbocyanine molecular beacons were prepared by homologation of reactive carboxyl groups of the beacon with imino diacetic acid. Their conjugation with unprotected d-(+)-glucosamine gave dendritic arrays of the carbohydrate on an inner NIR chromophore core. In vivo evaluation of the dendritic glucosamine constructs shows enhanced uptake in proliferating tumor cells relative to surrounding normal tissue. The structural framework of these polyvalent beacons permits the amplification by synergistic effects of a variety of bioactive motifs or chemical sensors in molecular recognition interactions without dramatic change of their desirable NIR spectral properties.     

Two-dimensional molecular space with regular molecular structure

A novel two-dimensional molecular space (layered carboxylpropylamidephenylsilica, CPAPhS) with regular carboxyl groups was successfully synthesized through grafting carboxyl groups in the structure of layered (aminophenyl)silica using butanedioic anhydride. The carboxyl groups regularly arranged in the layered CPAPhS can react with various organic molecules with amino and hydroxyl groups through formation of reactive intermediate with catalyzers, such as SOCl2. In this research, an example was used to prove the reaction properties of regular carboxyl groups in layered CPAPhS. The layered CPAPhS was reacted with SOCl2 to form layered acyl chloridepropylamidephenylsilica (ACPAPhS) and then reacted with n-butylamine and n-butyl alcohol to form layered n-butylamidepropylamidephenylsilica (BAPAPhS) and n-butylesterpropylamidephenylsilica (BEPAPhS) with regular molecular structures. Layered CPAPhS showed the potential as a starting material for formation of a series of novel two-dimensional molecular space with various regular molecular structures, and as a solid acceptor for chemical reagent with amino and hydroxyl groups for chemical processes.     

Modified molecular charge similarity indices for choosing molecular analogues

Toward the goal of defining a molecular charge similarity idex that best quantifies the concept of molecular similarity as it relates to biological activity, we have evaluated a variety of definitions of the molecular charge distribution function, ρ, for use in the charge similarity index formalism. Spatially distributed nuclear charges are incorporated into electron distribution functions to approximately account for the screening of core electronic charge and to model the net effect of the total charge distribution in a manner that better reflects the inherent relation to the molecular electrostatic potential. The resulting charge similarity indices are evaluated based on their sensitivity to relative molecule displacement and their ability to meaningfully group or order a simple set of molecular structures: CH₃CH₂CH₃, CH₃OCH₃, and CH₃SCH₃.     

Examination of stabilty of molecular agglomerates in molecular crystals

We report an examination algorithm of stability of molecular aggregates based on the estimation of rigidity of intermolecular contacts in a crystal structure. The algorithm includes the intermolecular interaction energy calculation (in the atom-atom potential approximation) of a pair of molecules selected in the crystal structure. Further, the energy is minimized using a least-squares technique by varying the position and orientation of one of the molecules. The contact rigidity is quantitatively assessed by the minimized rms difference between the positions of the atoms in the original and optimized structures (Zorkii’s criterion). Every rigid contact revealed in the structure determines finite or infinite stable agglomerates. The paper presents the results of testing the computer program based on this algorithm with a number of real crystal structures previously determined by single crystal X-ray diffraction, and also the examples of the most common stable molecular agglomerates found with the aid of the program.     

Interfacial nanoarchitectonics for molecular manipulation and molecular machine operation

The nanoarchitectonics concept enables us to produce functional systems and materials from nanoscale units through nanotechnological approaches together with the processes including chemical syntheses, atom/molecule manipulations, self-assemblies, self-organizations, field-induced material regulations, and bio-related processes. Especially, manipulations of molecules (molecular machines) and sophisticated organization would be attractive targets in interfacial nanoarchitectonics. In this short review, we introduce several typical examples on manipulations of functional molecules and molecular machines at interfacial media. The examples are classified roughly according to driving forces of manipulations; (i) manipulations through chemical reactions and interactions; (ii) light-driven manipulations; (iii) electrically controlled manipulations; (iv) mechanical manipulations. Future possibilities of molecular manipulations at interfaces such as usages in biological systems are discussed in perspective section.     

Diels-Alder via molecular recognition in a crystalline molecular flask

In the pore of a porous coordination network, Diels-Alder reactants, a diene and a dienophile, are recognized by donor-acceptor and multiple H-bond interactions, respectively, and fixed at ideal positions for the reaction. Heating the crystals promoted the Diels-Alder reactions with enhanced reactivity and controlled regioselectivity as clearly monitored by in situ X-ray crystallography.     

Gaussian expansion method for molecular integrals of molecular properties

The finite Gaussian Expansion method for molecular integrals proposed by Taketa, O-ohata and Huzinaga has been extended to the integrals of molecular properties. The integral formulas of so-called moment, field and field gradient integrals have been derived. It has been numerically shown that in order to evaluate the field and the field gradient integrals based on Slater type orbitals, eight- or ten-term Gaussian expansions are sufficient but this method fails to attain sufficient effective numbers for the moment integrals.     

Thermal conductivities of molecular liquids by reverse nonequilibrium molecular dynamics

The reverse nonequilibrium molecular dynamics method for thermal conductivities is adapted to the investigation of molecular fluids. The method generates a heat flux through the system by suitably exchanging velocities of particles located in different regions. From the resulting temperature gradient, the thermal conductivity is then calculated. Different variants of the algorithm and their combinations with other system parameters are tested: exchange of atomic velocities versus exchange of molecular center-of-mass velocities, different exchange frequencies, molecular models with bond constraints versus models with flexible bonds, united-atom versus all-atom models, and presence versus absence of a thermostat. To help establish the range of applicability, the algorithm is tested on different models of benzene, cyclohexane, water, and n-hexane. We find that the algorithm is robust and that the calculated thermal conductivities are insensitive to variations in its control parameters. The force field, in contrast, has a major influence on the value of the thermal conductivity. While calculated and experimental thermal conductivities fall into the same order of magnitude, in most cases the calculated values are systematically larger. United-atom force fields seem to do better than all-atom force fields, possibly because they remove high-frequency degrees of freedom from the simulation, which, in nature, are quantum-mechanical oscillators in their ground state and do not contribute to heat conduction.     

Chirality induction and protonation-induced molecular motions in helical molecular strands

The long oligopyridinedicarboxamide strand 9, containing 15 heterocyclic rings has been synthesized and its helical structure determined by X-ray crystallography. It was shown that the shorter analogue 6 displays induced circular dichroism and amplification of induced chirality upon dissolution in an optically active solvent, diethyl-L-tartrate. A novel class of helical foldamers was prepared, strands 14-16, based on two oligopyridine carboxamide segments linked through a L-tartaric acid derived spacer. These tartro strands display internal chirality induction as well as chirality amplification. NMR spectroscopy (on 8 and 9) and circular dichroism (on 16) studies show that the oligopyridine carboxamide strands undergo reversible unfolding/folding upon protonation. The protonation-induced unfolding has been confirmed by X-ray crystallographic determination of the molecular structure of the extended protonated heptameric form 8(+). The molecular-scale mechano-chemical motions of the protonation-induced structural switching consist of a change of the length of the molecule, from 6 angstroms (6, coiled form) to 29 angstroms (8(+), uncoiled form) for the heptamer and from 12.5 angstroms (9, coiled form, X-ray structure) to 57 angstroms (9(+), uncoiled form, from modeling) for the pentadecamer. Similar unfolding/folding motional processes take place in the L-tartro strands 15 and 16 upon protonation/deprotonation, with loss of helicity-induced circular dichroism on unfolding as shown for the protonated form 16(+).     

Hybrid molecular material exhibiting single-molecule magnet behavior and molecular conductivity

Two unique materials based on Mn4 single-molecule magnet (SMM) clusters (ST=9) and integer or non-integer average valent platinum maleonitriledithiolate (mnt2-) complexes, [{MnII2MnIII2(hmp)6(MeCN)2}{Pt(mnt)2}2][Pt(mnt)2]2.2MeCN (1) and [{MnII2MnIII2(hmp)6(MeCN)2}{Pt(mnt)2}4][Pt(mnt)2]2 (2), were synthesized by the material diffusion method and electrochemical oxidation, respectively (hmp-=2-hydroxymethylpyridinate). 1 and 2 are comprised of four and six [Pt(mnt)2]n- units, respectively, in addition to a common MnII2MnIII2 double-cuboidal unit, [MnII2MnIII2(hmp)6(MeCN)2]4+ (hereinafter [Mn4]4+). Among the [Pt(mnt)2]n- units, two units in 1 and four units in 2 are coordinated with the [Mn4]4+ unit, forming a 1D chain of {-[Mn4]-[Pt(mnt)2]2-} for 1 and a discrete subunit of {[Pt(mnt)2]2-[Mn4]-[Pt(mnt)2]2} for 2. The other two [Pt(mnt)2]n- units, occupying void space of the packing, form a stacking column with the coordinating [Pt(mnt)2]n- units, finally constructing hybrid frames of aggregates consisting of [Mn4]4+ units and [Pt(mnt)2]n- units. Electronic conductivity measurements revealed that 1 is an insulator and 2 is a semiconductor with sigma=0.22 S.cm(-1) at room temperature and an activation energy of 136 meV. Detailed magnetic measurements proved that the [Mn4]4+ units in 1 and 2 behave as SMMs with an ST=9 ground state at low temperatures. There is no significant interaction between [Mn4]4+ units and [Pt(mnt)2]n- units, but interactions between localized spins of [Pt(mnt)2]n- were detected even in 2 at low temperatures where the conductivity is electronically insulated. 2 is the first example of a hybridized material exhibiting SMM behavior and electronic conductivity.     

The kinetic energy of molecular charge distributions and molecular stability

This paper examines the relationship between the topographical features of a molecular charge distribution and the kinetic energy of the system. Specifically, the spatial contributions to the kinetic energy are related to the Laplacian of the total charge density and to the gradients of the natural-orbital densities. It is concluded that a necessary requirement for molecular stability is the existence of a net negative curvature for the molecular charge distribution in the internuclear region. It is shown that the charge density accumulated in the internuclear region of a stable molecule is distributed in such a way as to keep the accompanying increase in the kinetic energy to a minimum. A comparison of the contributions to the kinetic energy from the atomic and molecular charge distributions indicates that in the formation of a stable molecule the contribution from the molecular charge density in the binding region is decreased relative to that of the atoms.     

Ortho-selectivity in aluminophosphate molecular sieves: A molecular simulation study

Monte Carlo adsorption simulations of xylenes have been performed in aluminophosphate molecular sieve structures. A new force field fitted for o-xylene in AlPO₄-5 was used. It is shown that force fields have good transferability among the aluminophosphate sieves series and the new force field adequately describes the experimentally observed adsorption isotherms for xylene/AlPO₄-5. A previous investigation of adsorption isotherms and structural analysis has been extended to AlPO₄-8 and VPI-5 sieves. In AlPO₄-8, like in AlPO₄-5, the variations in the channels diameters and the corresponding interaction energy of the molecule-crystal lattice drive all molecular positioning. In VPI-5, the modulation between wide and narrow regions becomes negligible due to the larger pore diameter, so no ortho-selectivity was observed. The simulations confirm the ortho-selectivity mechanism proposed to aluminophosphates.     

Fine tuning of molecular rotor function in photochemical molecular switches

Molecular switches are used as scaffolds for the construction of controlled molecular rotors. The internal position of the switching entity in the molecule controls the dynamic behaviour of the rotor moiety in the molecule. Six new molecular motors with o-xylyl rotor moieties were prepared on the basis of an overcrowded alkene, and their dynamics were systematically studied by 2D EXSY NMR. Variation of the (hetero-)atoms in the upper and lower halves of the overcrowded alkene allows fine tuning of the rate of rotation of the o-xylyl rotor in the lower half of the molecule. For all rotors it was observed that the rotation barrier for the trans-isomer was higher than that of the corresponding cis-isomer. The results are analyzed and discussed in terms of differences in steric interactions in the presented system.     

Net signs of molecular graphs: Dependence of molecular structure

The concept of internal connectivity associates to each eigenvector of the molecular graph a graph with signed edges. We show that the respective edge signs can be deduced without knowing the graph eigenvectors. The dependence of the edge signs on molecular structure is elucidated. The sign of an edge whose end vertices are ν_r and ν_s is found to be the result of separate interactions through all paths connecting the vertices ν_r and ν_s. The analysis of the edge signs is particularly simple in the case of acyclic systems. © 1994 John Wiley & Sons, Inc.