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.     

Determination of molecular weight dependences and characterization of molecular weight distributions

Molecular weight dependences of the square of the radius of gyration as well as of the coefficients of diffusion and friction of monodisperse polystyrenes in toluene at 20°C are determined experimentally. For this purpose, the z-averages of these quantities and $\text{M}$_w as determined by light scattering were subjected to the polydispersity correction procedures as described previously. In addition, a method is suggested for the checking of known data with respect to molecular weight distribution, using measured values in conjunction with the polydispersity correction procedures.     

Prediction of molecular volume and surface of alkanes by molecular topology

Molecular volume and molecular surface are expressed as a function of topological degree in alkane graphs. This allows not only a straightforward approach to calculate such physicochemical magnitudes but also an interpretation of the role of the local vertex invariant (LOVI) or valence degree, delta, as well as the connectivity indices in the prediction of physicochemical properties. The interpretation is based on the concept of molecular accessibility (as introduced by Estrada, J. Phys. Chem. A 2002, 106, 9085) for which precise mathematical definitions are provided.     

Design and evaluation of a crystalline hybrid of molecular conductors and molecular rotors

Combining recent concepts from the fields of molecular conductivity and molecular machinery we set out to design a crystalline molecular conductor that also possesses a molecular rotor. We report on the structures, electronic and physical properties, and dynamics of two solids with a common 1,4-bis(carboxyethynyl)bicyclo[2.2.2]octane (BABCO) functional rotor. One, [nBu(4)N(+)](2)[BABCO][BABCO(-)](2), is a colorless insulator where the dicarboxylic acid cocrystallizes with two of its monoanionic conjugated bases. The other is self-assembled by electrocrystallization in the form of black, shiny needles, with highly conducting molecular slabs of (EDT-TTF-CONH(2))(2)(+) (EDT-TTF = ethylenedithiotetrathiafulvalene) and anionic [BABCO(-)] rotors. Using variable-temperature (5-300 K) proton spin-lattice relaxation, (1)H T(1)(-1), we were able to assign two types of Brownian rotators in [nBu(4)N(+)](2)[BABCO][BABCO(-)](2). We showed that neutral BABCO groups have a rotational frequency of 120 GHz at 300 K with a rotational barrier of 2.03 kcal mol(-1). Rotors on the BABCO(-) sites experience stochastic 32 GHz jumps at the same temperature over a rotational barrier of 2.72 kcal mol(-1). In contrast, the BABCO(-) rotors within the highly conducting crystals of (EDT-TTF-CONH(2))(2)(+)[BABCO(-)] are essentially "braked" at room temperature. Notably, these crystals possess a conductivity of 5 S cm(-1) at 1 bar, which increases rapidly with pressure up to 50 S cm(-1) at 11.5 kbar. Two regimes with different activation energies E(a) for the resistivity (180 K above 50 and 400 K below) are observed at ambient pressure; a metallic state is stabilized at ca. 8 kbar, and an insulating ground state remains below 50 K at all pressures. We discuss two likely channels by which the motion of the rotors might become slowed down in the highly conducting solid. One is defined as a low-velocity viscous regime inherent to a noncovalent, physical coupling induced by the cooperativity between five C(sp3)-H···O hydrogen bonds engaging any rotor and five BABCO units in its environment. The rotational barrier calculated with the effect of this set of hydrogen bonds amounts to 7.3 kcal mol(-1). Another is quantum dissipation, a phenomenon addressing the difference of dynamics of the rotors in the two solids with different electrical properties, by which the large number of degrees of freedom of the low dimensional electron gas may serve as a bath for the dissipation of the energy of the rotor motion, the two systems being coupled by the Coulomb interaction between the charges of the rotors (local moments and induced dipoles) and the charges of the carriers.     

Calculations of molecular properties in hybrid coupled-cluster and molecular mechanics approach

We report benchmark calculations obtained with our new coupled-cluster singles and doubles (CCSD) code for calculating the first- and second-order molecular properties. This code can be easily incorporated into combined [Valiev, M.; Kowalski, K. J. Chem. Phys. 2006, 125, 211101] classical molecular mechanics (MM) and ab initio coupled-cluster (CC) calculations using NWChem, enabling us to study molecular properties in a realistic environment. To test this methodology, we discuss the results of calculations of dipole moments and static polarizabilities for the Cl2O system in the CCl4 solution using the CCSD (CC with singles and doubles) linear response approach. We also discuss the application of the asymptotic extrapolation scheme (AES) [Kowalski, K.; Valiev, M. J. Phys. Chem. A 2006, 110, 13106] in reducing the numerical cost of CCSD calculations.     

Ratios of average molecular weights and molecular weight distributions in polymers

If M_min and M_max are lower and upper bounds, respectively, to the molecular weights of different molecular weight species contained in a polymer, the weight-average to number-average molecular weight ratio M _w/M _n cannot exceed (1 + M_max/M_min)²/(4M_max/M_min). The ratio attains this maximum possible value if the masses of the two species with molecular weights M_min and M_max are equal and the masses of all the other species are negligibly small, corresponding to maximum spread in the molecular weight distribution within the specified bounds. Also for a given value of M _w/M _n = α, the M_max cannot be smaller than [2α ? 1 + 2α^1/2(α ? 1)^1/2]M_min. The minimum possible value of M_max/M_min consistent with α given is obtained in the case of maximum spread described above. If only one species is predominant, then both M _w/M _n and M_max/M_min approach unity, as is well known. Similar relations hold for the ratios of higher-order average molecular weights for which the role of the mass fractions is replaced by higher-order distribution functions.     

Balance of xanthophylls molecular and protonated molecular ions in electrospray ionization

This paper reports the chemical evidence of the balance between radical molecular ions and protonatedmolecules of xanthophylls (an oxygen-containing carotenoid) with a conjugated pi-system (polyene) and oxygen as a heteroatom in ESI and HRESI mass spectrometry. The ionization energy of neutral xanthophylls was calculated by semi-empirical methods. The results were compared with those previously published for carotenoids and retinoids, which have also been shown in ESI-MS to form M(+*) and [M + H](+), respectively. This study demonstrates, for the first time, the correlation of an extended conjugation and the presence of oxygen in the formation and balance of M(+*) or [M + H](+) for the carotenoids, neoxanthin, lutein, violaxanthin and zeaxanthin.     

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.     

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.     

Structural analysis of porphyrin molecular squares using molecular mechanics and density-functional methods

"Molecular squares" formed from Re(CO)(3)Cl corners and porphyrin sides have potential applications as hosts for catalytic sites and as building blocks for membranes. In these materials, knowledge of the conformations of the squares is important. Molecular-mechanics (MM) and density-functional (DF) calculations have been used iteratively in this work to find the minimum-energy configurations of several porphyrin molecular squares. MM predicts that the steric and torsional interactions at connecting junctures of the square framework determine the overall geometry. Torsional degrees of freedom around these junctures were therefore analyzed using DF methods, giving further insight and helping choose among MM force-field options. Single-point DF calculations on the entire squares showed that the energy and conformation of the entire square could be reliably obtained by performing DF calculations on the critical elements of the square and then piecing them together. This "piecewise" strategy allows for both the major torsional motions and the most important local relaxations of large supramolecular species such as molecular squares.     

Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods

Summary Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte> MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the phenyl ring rotational barrier for neutral MP and gave results very similar to those of the HF/6-31G* method.     

Dephasing of molecular vibrations in liquids: Effects of molecular orientations and attraction

An equation for vibrational dephasing rates in liquids containing the effects of molecular orientations and attraction has been derived by use of the binary collision model. Dephasing rates are found to be a strong function of the orientation angle of vibrating molecules. For liquid nitrogen, the inclusion of oriented encounters leads to a slowing down of the dephasing rate by a factor of about three. Molecular attraction is found to enhance dephasing significantly.     

Solvent and hydrogen confinement in molecular capsules-Hirshfeld surface and molecular simulation analysis

Hirshfeld surface analysis of the 'ordered' inner phase of the molecular capsule complex, [(chloroform)(6)@C-n-butylpyrogallol[4]arene)(6)], provides insight into the intermolecular contacts and orientation of the solvent molecules. Molecular simulations show that adding two or three hydrogen molecules to the six solvent molecules is energetically favoured, and this correlates with NMR studies.     

Theoretical molecular predictions and antimicrobial activities of newly synthesized molecular hybrids of norfloxacin and ciprofloxacin

Antibiotics such as norfloxacin and ciprofloxacin are used to treat numerous bacterial infections. The present research work involves the molecular prediction, synthesis, characterization and in vitro antimicrobial activities of molecular hybrids of norfloxacin and ciprofloxacin. First set of compounds involve the substitutions of various amines at third position of ciprofloxacin and norfloxacin. On the other hand, second set of molecular hybrids include the substitution of different amines at seventh position along with linker (─COCH₂─). These synthesized compounds were identified by TLC technique and well characterized by various spectroscopic techniques such as IR, NMR, and ESI-MS. Molecular prediction of these newly synthesized compounds have been carried out using the SwissADME, ADMETLab software. Their cytotoxicity parameters have also been studied using Osiris software. It was observed that almost all these molecular hybrids suitable for their drug likeness properties. Further, these newly synthesized compounds were subjected to study their antimicrobial activities in vitro. The third substituted as well as most of seventh substituted molecular hybrids have shown 10-folds increase in their antibacterial activity as compared to the standard drug ciprofloxacin. Some of these compounds have also shown their potency when subjected to study their cytotoxicity test against Escherichia coli AB 1157, proficient to prepare damage in DNA.     

Valency and molecular structure

Valency is defined for each molecular orbital. The molecular orbital valency values are shown to be a good measure of the bonding nature of the molecular orbital. Comparisons are made with photoelectron spectral studies and Mulliken overlap population analysis.The variation of molecular valency and molecular orbital valency with bond angle is studied. It is found that for all the molecules presently considered, energy is linearly related to valency and that the molecular valency reaches a maximum at the equilibrium bond angle. It is also shown that the molecular orbital valency can serve as a quantitatively reliable ordinate for Mulliken-Walsh diagrams.