Rapid topography mapping of scalar fields: Large molecular clusters

An efficient and rapid algorithm for topography mapping of scalar fields, molecular electron density (MED) and molecular electrostatic potential (MESP) is presented. The highlight of the work is the use of fast function evaluation by Deformed-atoms-in-molecules (DAM) method. The DAM method provides very rapid as well as sufficiently accurate function and gradient evaluation. For mapping the topography of large systems, the molecular tailoring approach (MTA) is invoked. This new code is tested out for mapping the MED and MESP critical points (CP's) of small systems. It is further applied to large molecular clusters viz. (H(2)O)(25), (C(6)H(6))(8) and also to a unit cell of valine crystal at MP2∕6-31+G(d) level of theory. The completeness of the topography is checked by extensive search as well as applying the Poincare?-Hopf relation. The results obtained show that the DAM method in combination with MTA provides a rapid and efficient route for mapping the topography of large molecular systems.     

Absorption and emission properties of 5-phenyl tris(8-hydroxyquinolinato) M(III) complexes (M = Al,Ga, In) and correlations with molecular electrostatic potential

Substituent effect for a series of 5-phenyl tris(8-hydroxyquinolinato) M(III) complexes (Mq3) of aluminum, gallium, and indium are investigated using density functional theory (DFT) for the ground state properties and the time-dependent version of DFT (TDDFT) for their absorption and emission properties. A comparison between the ground state energy of mer and fac isomers of all the complexes revealed that the mer configuration is always more stable than fac. The substituent effect is significantly reflected at the fluorescence maximum (λ_F) values whereas the effect is moderate at the absorption maximum (λ_abs) values. The molecular electrostatic potential (MESP) at the metal center (V_M) and the most electron rich region indicated by MESP minimum (V_min), located at the oxygen of phenoxide ring exhibit excellent correlations with the λ_F and Stokes shift (λ_F−λ_abs) values. The study suggests the use of Stokes shift as an experimental quantity to measure the excited state substituent effect while the V_min or V_M emerge as theoretical quantities to measure the same.     

Topography of scalar fields: molecular clusters and π-conjugated systems

The pioneering works due to Bader and co-workers have generated widespread interest in the study of the topography of molecular scalar fields, the first step of which is the identification and characterization of the corresponding critical points (CPs). The topography of a molecular system becomes successively richer in going from the bare nuclear potential (BNP) to the molecular electrostatic potential (MESP) through the molecular electron density (MED). The present work clearly demonstrates, through the study of some π-conjugated test molecules as well as molecular clusters, that the CPs could be economically located by following this path within ab initio level theory. Further, the topography mapping of large molecules, especially at a higher level of theory, is known to be a demanding task. However, it is rendered possible by following the above sequential mapping assisted by a divide-and-conquer-type method termed as the molecular tailoring approach (MTA). This is demonstrated with the topography mapping of β-carotene and benzene nonamer at MP2 and a (H(2)O)(32) cluster at the HF level of theory, which are rather challenging problems with contemporary off-the-shelf computer hardware.     

Topography of approximate molecular electrostatic potentials

A new method is described for the approximation of the molecular electrostatic potential (MESP). This method is used for the study of the topography of small molecules. The critical points of the approximate and the exact MESP are compared. It is found that most of the critical points of the exact MESP are retained, but in regions where the exact MESP changes slowly near critical points the number of critical points of the approximate MESP can be reduced.     

Prelude to molecular dynamics: Topography-driven gaussian charge models

A new strategy to develop Gaussian charge models (GCMs) for molecules like ammonia, water, ethene, hydrogen sulfide, formaldehyde and benzene is presented. These molecular models comprising of positive point charges and negative Gaussian charge distributions (GCDs), which represent nuclei and continuous electron charge distribution, are found to correctly represent the ab initio Molecular Electrostatic Potential (MESP) and reproduce its essential topographical features of corresponding molecules. The models use optimized parameters: positive charges at nuclei, negative charges on GCDs, Gaussian exponent and centers. The Potential Energy Surface (PES) of water dimer has been explored using water GCMs. A good agreement has been found between PES obtained using GCMs and wave function. The Gaussian models correctly predict structure of benzene-water complex. It is thus recommended to use GCMs for molecular dynamic simulations.     

nMoldyn 3: Using task farming for a parallel spectroscopy‐oriented analysis of molecular dynamics simulations

We present a new version of the program package nMoldyn, which has been originally developed for a neutron‐scattering oriented analysis of molecular dynamics simulations of macromolecular systems (Kneller et al., Comput. Phys. Commun. 1995, 91, 191) and was later rewritten to include in‐depth time series analyses and a graphical user interface (Rog et al., J. Comput. Chem. 2003, 24, 657). The main improvement in this new version and the focus of this article are the parallelization of all the analysis algorithms for use on multicore desktop computers as well as distributed‐memory computing clusters. The parallelization is based on a task farming approach which maintains a simple program structure permitting easy modification and extension of the code to integrate new analysis methods. © 2012 Wiley Periodicals, Inc.     

CERES: An ab initio code dedicated to the calculation of the electronic structure and magnetic properties of lanthanide complexes

We have developed and implemented a new ab initio code, Ceres (Computational Emulator of Rare Earth Systems), completely written in C++11, which is dedicated to the efficient calculation of the electronic structure and magnetic properties of the crystal field states arising from the splitting of the ground state spin‐orbit multiplet in lanthanide complexes. The new code gains efficiency via an optimized implementation of a direct configurational averaged Hartree–Fock (CAHF) algorithm for the determination of 4f quasi‐atomic active orbitals common to all multi‐electron spin manifolds contributing to the ground spin‐orbit multiplet of the lanthanide ion. The new CAHF implementation is based on quasi‐Newton convergence acceleration techniques coupled to an efficient library for the direct evaluation of molecular integrals, and problem‐specific density matrix guess strategies. After describing the main features of the new code, we compare its efficiency with the current state–of–the–art ab initio strategy to determine crystal field levels and properties, and show that our methodology, as implemented in Ceres , represents a more time‐efficient computational strategy for the evaluation of the magnetic properties of lanthanide complexes, also allowing a full representation of non‐perturbative spin‐orbit coupling effects. © 2017 Wiley Periodicals, Inc.     

Adsorption of water on sodium chloride surfaces: electrostatics – guided ab initio studies

Water adsorption is studied on medium-sized clusters of sodium chloride representing (100) and (110) surfaces at the ab initio level. Topographical features of molecular electrostatic potential (MESP) have been employed for predicting the potent sites for binding of one to four water molecules on these surfaces. Such guess geometries are initially optimized using an electrostatics-based model, electrostatic potential for intermolecular complexation (EPIC) and further at the Hartree–Fock and B3LYP/6-31G(d, p) levels. The corresponding interaction energies are examined for assessing co-operative binding effects. The geometry and interaction energy of four water molecules adsorbed on NaCl(100) clearly brings out the co-operative binding among the water molecules. Further, water binding to (110) surface is stronger than that with (100) surface. This is also in confirmation with the electrostatic properties of (110) surface. Many-body decomposition analysis brings out the stronger interaction between NaCl clusters with water molecules vis-a-vis water–water interaction.     

Theoretical studies on the carcinogenicity of polycyclic aromatic hydrocarbons

The distinct molecular regions of a set of 28 polycyclic aromatic hydrocarbons (PAHs) showing varying degrees of carcinogenic activity (CA) have been analyzed on the basis of their calculated molecular electrostatic potential (MESP) at B3LYP/6-31+G(d,p) level of theory. The MESP, being a property directly related to electron density, clearly distinguishes the electron dense centers in the molecule into K, L, M, and newly defined N regions. Further, a quantitative structure activity relationship (QSAR) model of carcinogenicity is developed using the volume of MESP lobes at the named regions for a set of 17 carcinogenic molecules with experimentally known CA index. The QSAR equation suggested that all the geometrical regions are significant in determining the carcinogenic property of PAHs. The model clearly showed that K and M regions have activating carcinogenic effect whereas L and N regions have deactivating carcinogenic effect. The CA showed considerable enhancement when any three distinct regions are present in a PAH. On the other hand, all the PAH systems with only one type of region are inactive irrespective of whether the region is activating or deactivating. Similarly, molecules showing the presence of two types of regions are either inactive or weakly active. The essential features of both the "K, L region" and the "bay region" theories of carcinogenesis are well evident in the new QSAR model, as the former theory works on the basis of activating K and deactivating L regions whereas the latter theory is related with the activating M region.     

Recent Advances of AIE-Active Conjugated Polymers: Synthesis and Application

Conjugated polymers (CPs) have long been recognized as an important class of materials. The highly conjugated backbone of the CPs will facilitate the rapid exciton migration and result in amplification of fluorescence signals. However, CPs are likely to aggregate and form excimers in solid states, directly leading to the fluorescence quenching, namely aggregation-caused quenching (ACQ), hence inhibiting their prospective utilizations in a large degree. Since the effect of aggregation-induced emission (AIE) is opposite to that of notorious ACQ, the AIE has raised great attention from scientists. CPs with AIE or aggregation-enhanced emission (AEE) features may help to solve the ACQ problem and meanwhile impart polymers with new properties and practical applications. In this review, we summarize the recent progress on the preparation of CPs with AIE or AEE characteristics, where AIE-active luminogens are located at polymer backbones or pendants. Their potential applications including fluorescent sensors, biological probes, and active layers for the fabrication of light-emitting diodes are also described.     

A New Dimension for Coordination Polymers and Metal–Organic Frameworks: Towards Functional Glasses and Liquids

There are two categories of coordination polymers (CPs): inorganic CPs (i‐CPs) and organic ligand bridged CPs (o‐CPs). Based on the successful crystal engineering of CPs, we here propose noncrystalline states and functionalities as a new research direction for CPs. Control over the liquid or glassy states in materials is essential to obtain specific properties and functions. Several studies suggest the feasibility of obtaining liquid/glassy states in o‐CPs by design principles. The combination of metal ions and organic bridging ligands, together with the liquid/glass phase transformation, offer the possibility to transform o‐CPs into ionic liquids and other ionic soft materials. Synchrotron measurements and computational approaches contribute to elucidating the structures and dynamics of the liquid/glassy states of o‐CPs. This offers the opportunity to tune the porosity, conductivity, transparency, and other material properties. The unique energy landscape of liquid/glass o‐CPs offers opportunities for properties and functions that are complementary to those of the crystalline state.     

RMC_POT: A computer code for reverse monte carlo modeling the structure of disordered systems containing molecules of arbitrary complexity

An approach has been devised and tested for preserving the molecular dynamics molecular geometry taking into account energetic considerations during Reverse Monte Carlo (RMC) modeling. Instead of the commonly used fixed neighbor constraints, where molecules are held together by constraining distance ranges available for the specified atom pairs, here molecules are kept together via bond, angle, and dihedral potential energies. The scaled total potential energy contributes to the measure of the goodness‐of‐fit, thus, the atoms can be prevented from drifting apart. In some of the calculations (Lennard‐Jones and Coulombic) nonbonding potentials were also applied. The algorithm was successfully tested for the X‐ray structure factor‐based structure study of liquid dimethyl trisulfide, for which material now significantly more sensible results have been obtained than during previous attempts via any earlier version of RMC modeling. It is envisaged that structural modeling of a large class of materials, primarily liquids and amorphous solids containing molecules of up to about 100 atoms, will make use of the new code in the near future. © 2012 Wiley Periodicals, Inc.     

Orbital topology. II. Orbital mapping of unsymmetrical molecules. A survey of the thermal isomerizations of dewar isomers of isoelectronically substituted benzenes,cyclopentadienes, and cyclopentadienyl ions

Orbital mapping analysis, based on EHT and CNDO/2 semiempirical molecular orbitals, has been used to survey the thermal, disrotatory, ring-opening isomerizations of bicyclo[2.2.0]hexa-2,5-dienes (Dewar benzenes), bicyclo[2.1.0]pent-2-enes, and bicyclo[2.1.0]pent-2-en-5-yl ions to their planar isomers. Results indicate that isoelectronic substitution (CH replaced by C^?, O⁺, N, NH⁺, etc.) in the molecular framework may favor allowed thermal reactions in some cases, in contrast to the disallowed reaction predicted for the parent hydrocarbons.     

Structure, reactivity and aromaticity of acenes and their BN analogues: a density functional and electrostatic investigation

Density functional calculations have been carried out on a series of linearly annelated acenes and their BN analogues. Even though borazine shows aromatic and reactivity behavior parallel with that of benzene, its condensed derivatives show patterns different from those of their hydrocarbon analogues. Nucleus independent chemical shift (NICS) values in acenes suggest that the aromaticity of the inner rings is more than that of benzene, whereas in BN-acenes there is no substantial change in the aromaticity of the individual rings. Molecular electrostatic potential (MESP) is employed to obtain further insights into the bonding and reactivity trends for these systems. The MESP topography patterns of acenes and BN-acenes are substantially different, with BN-acenes showing more localized pi electron features compared to those of acenes. The MESP values at the critical points (CPs) indicate overall lowering of aromaticity in these annelated systems. However, this change is gradual among the BN-acenes.     

Method and algorithm of obtaining the molecular intrinsic characteristic contours (MICCs) of organic molecules

The molecular intrinsic characteristic contour (MICC) is defined as the set of all the classical turning points of electron movement in a molecule. Studies on the MICCs of some medium organic molecules, such as dimethylether, acetone, and some homologues of alkanes, alkenes, and alkynes, as well as the electron density distributions on the MICCs, are shown for the first time. Results show that the MICC is an intrinsic approach to shape and size of a molecule. Unlike the van der Waals hard-sphere model, the MICC is a smooth contour, and it has a clear physical meaning. Detailed investigations on the cross-sections of MICCs have provided a kind of important information about atomic size changing in the process of forming molecules. Studies on electron density distribution on the MICC not only provide a new insight into molecular shape, but also show that the electron density distribution on the boundary surface relates closely with molecular properties and reactivities. For the homologues of alkanes, Rout(H), Dmin, and Dmax (the minimum and maximum of electron density on the MICC), all have very good linear relationships with minus of the molecular ionization potential. This work may serve as a basis for exploring a new reactivity indicator of chemical reactions and for studying molecular shape properties of large organic and biological molecules.     

Conjugated Oligomers and Polymers Sheathed with Designer Side Chains

Conjugated polymers (CPs) are often referred to as molecular wires because of their quasi one‐dimensional electronic wavefunctions delocalized along the polymer chains. However, in the solid state, CPs tend to self‐assemble through π‐stacking, which greatly attenuates the one‐dimensional nature. By molecular design, CPs can be molecularly insulated just like electric power cords, resulting in so‐called “insulated” molecular wires (IMWs). In this Focus Review, we will discuss their unique photophysical, electronic, and mechanical properties which originate from the absence of π‐stacking.     

Accurate and fast algorithm of the molecular incomplete gamma function with a complex argument

Several efficient algorithms for the accurate and fast calculation of the molecular incomplete gamma function Fm(z) with a complex argument z are developed. The complex incomplete gamma function is arising in molecular integrals over the gauge-including atomic orbitals. Two kinds of algorithms are recommended: (1) a high-precision version and (2) a fast version. The high-precision version is able to guarantee 15 significant figures (10(-15) in the relative error) and the fast version is able to guarantee 12 significant figures (10(-12) in the relative error), at worst, within the double-precision arithmetic. The fast version is about 5-20 times faster than the high-precision version. For most molecular calculations, the fast version will give a satisfied precision.     

Molecular electrostatic potential for exploring π-conjugation: a density-functional investigation

Molecular electrostatic potentials (MESP) of the most common building blocks of organic π-conjugated systems, viz. ethylene, acetylene, benzene, furan, pyrrole, thiophene and phenylvinylene, are examined at the B3LYP/6-311++G(2d,2p) level. The topography of MESP is employed for mapping the strength of electronic conjugation between these building blocks. When electron-rich molecular regions are connected to each other, the MESP value of the corresponding conjugation critical point (CCP) is able to provide a quantitative measure of the strength of the conjugation. The systems with stronger conjugation are generally seen to possess a larger negative value of CCP and a smaller difference (ΔV(CM-CCP)) between the MESP values of respective conjugated minimum (CM) and the CCP, in agreement with the experimental as well as other theoretical results. The present MESP topography-based approach thus offers a measure of the quantitative strength of π-conjugation in molecules.     

Monte Carlo simulation algorithm for B‐DNA

Understanding the structure–function relationship of biomolecules containing DNA has motivated experiments aimed at determining molecular structure using methods such as small‐angle X‐ray and neutron scattering (SAXS and SANS). SAXS and SANS are useful for determining macromolecular shape in solution, a process which benefits by using atomistic models that reproduce the scattering data. The variety of algorithms available for creating and modifying model DNA structures lack the ability to rapidly modify all‐atom models to generate structure ensembles. This article describes a Monte Carlo algorithm for simulating DNA, not with the goal of predicting an equilibrium structure, but rather to generate an ensemble of plausible structures which can be filtered using experimental results to identify a sub‐ensemble of conformations that reproduce the solution scattering of DNA macromolecules. The algorithm generates an ensemble of atomic structures through an iterative cycle in which B‐DNA is represented using a wormlike bead–rod model, new configurations are generated by sampling bend and twist moves, then atomic detail is recovered by back mapping from the final coarse‐grained configuration. Using this algorithm on commodity computing hardware, one can rapidly generate an ensemble of atomic level models, each model representing a physically realistic configuration that could be further studied using molecular dynamics. © 2016 Wiley Periodicals, Inc.     

Membrane Filtration of Iron(III), Copper(II) and Lead(II) Ions as 1‐(2‐Pyridylazo) 2‐Naphtol (PAN) for Their Preconcentration and Atomic Absorption Determinations

A membrane filtration procedure for the preconcentration and atomic absorption spectrometric determination of Pb(II), Co(II) and Fe(III) ions in natural water samples has been established. Cellulose nitrate membrane filters (0.45 μm and 47 mm diameter) were used in all experiments. The procedure is based on chelate formation of the analyte metals with 1‐(2‐pyridylazo) 2‐naphtol (PAN) and on retention of the chelates on cellulose nitrate membrane filter. The cellulose nitrate membrane and analyte ions were completely dissolved by 500 μL of nitric acid at 85 °C on a hood and then metal determinations were performed by flame atomic absorption spectrometry. The method was applied to natural water samples for the determination of analyte ions with satisfactory results, e.g., recoveries > 95%, RSD's < 10%.