Molecular cluster building algorithm: electrostatic guidelines and molecular tailoring approach

Nano-sized clusters of various materials are recent experimental targets, since they exhibit size-dependent physico-chemical properties. A vast amount of literature is available on the study of molecular clusters but general methods for systematic evolution of their growth are rather scarce. The present work reports a molecular cluster building algorithm based on the electrostatic guidelines, followed by ab initio investigations, enabled by the application of molecular tailoring approach. Applications of the algorithm for generating geometries and interaction energies of large molecular clusters of zinc sulfide, benzene, and water are presented.     

Estimation of intramolecular hydrogen bond energy via molecular tailoring approach

A novel method, based on the molecular tailoring approach for estimating intramolecular hydrogen bond energies, is proposed. Here, as a case study, the O-H...O bond energy is directly estimated by addition/subtraction of the single point individual fragment energies. This method is tested on polyhydroxy molecules at MP2 and B3LYP levels of theory. It is seen to be able to distinguish between weak ( approximately 1 kcal mol(-1)) and moderately strong ( approximately 5 kcal mol(-1)) hydrogen bonds in polyhydroxy molecules.     

Intramolecular hydrogen bonding and cooperative interactions in carbohydrates via the molecular tailoring approach

In spite of many theoretical and experimental attempts for understanding intramolecular hydrogen bonding (H-bonding) in carbohydrates, a direct quantification of individual intramolecular H-bond energies and the cooperativity among the H-bonded networks has not been reported in the literature. The present work attempts, for the first time, a direct estimation of individual intramolecular O-H...O interaction energies in sugar molecules using the recently developed molecular tailoring approach (MTA). The estimated H-bond energies are in the range of 1.2-4.1 kcal mol(-1). It is seen that the OH...O equatorial-equatorial interaction energies lie between 1.8 and 2.5 kcal mol(-1), with axial-equatorial ones being stronger (2.0-3.5 kcal mol(-1)). The strongest bonds are nonvicinal axial-axial H-bonds (3.0-4.1 kcal mol(-1)). This trend in H-bond energies is in agreement with the earlier reports based on the water-water H-bond angle, solvent-accessible surface area (SASA), and (1)H NMR analysis. The contribution to the H-bond energy from the cooperativity is also estimated using MTA. This contribution is seen to be typically between 0.1 and 0.6 kcal mol(-1) when H-bonds are a part of a relatively weak equatorial-equatorial H-bond network and is much higher (0.5-1.1 kcal mol(-1)) when H-bonds participate in an axial-axial H-bond network.     

Ab initio investigation of benzene clusters: molecular tailoring approach

An exhaustive study on the clusters of benzene (Bz)(n), n = 2-8, at MP2/6-31++G(??) level of theory is reported. The relative strengths of CH-π and π-π interactions in these aggregates are examined, which eventually govern the pattern of cluster formation. A linear scaling method, viz., molecular tailoring approach (MTA), is efficiently employed for studying the energetics and growth patterns of benzene clusters consisting up to eight benzene (Bz) units. Accuracy of MTA-based calculations is appraised by performing the corresponding standard calculations wherever possible, i.e., up to tetramers. For benzene tetramers, the error introduced in energy is of the order of 0.1 mH (～0.06 kcal/mol). Although for higher clusters the error may build up, further corrections based on many-body interaction energy analysis substantially reduce the error in the MTA-estimate. This is demonstrated for a prototypical case of benzene hexamer. A systematic way of building up a cluster of n monomers (n-mer) which employs molecular electrostatic potential of an (n-1)-mer is illustrated. The trends obtained using MTA method are essentially identical to those of the standard methods in terms of structure and energy. In summary, this study clearly brings out the possibility of effecting such large calculations, which are not possible conventionally, by the use of MTA without a significant loss of accuracy.     

Structure, energetics, and reactivity of boric acid nanotubes: a molecular tailoring approach

Cardinality guided molecular tailoring approach (CG-MTA) [Ganesh et al. J. Chem. Phys. 2006, 125, 104019] has been effectively employed to perform ab initio calculations for large molecular clusters of boric acid. It is evident from the results that boric acid forms nanotubes, structurally similar to carbon nanotubes, with the help of an extensive hydrogen-bonding (H-bonding) network. Planar rosette-shaped hexamer of boric acid is the smallest repeating unit in such nanotubes. The stability of these tubes increases due to enhancement in the number of H-bonding interactions as the diameter increases. An analysis of molecular electrostatic potential (MESP) of these systems provides interesting features regarding the reactivity of these tubes. It is predicted that due to alternate negative and positive potentials on O and B atoms, respectively, boric acid nanotubes will interact favorably with polar systems such as water and can also form multiwalled tubes.     

Structures, energetics and vibrational spectra of CO2 clusters through molecular tailoring and cluster building algorithm

Clusters of CO(2) are a subject of detailed experimental as well as theoretical investigations due to their interesting applications. In the present article, CO(2) clusters (n = 6 to 13) are studied at the MP2 level of theory. The clusters are grown using a cluster building algorithm developed by our group and the larger ones are optimized at the MP2/aug-cc-pVDZ level by employing a Molecular Tailoring Approach (MTA). Vibrational spectra of these clusters are also calculated at this level of theory within MTA. The computed vibrational frequencies for an asymmetric C-O stretch generally exhibit a blue shift with increasing cluster size. This observation is in agreement with the experimental results. MTA-single point energies for each cluster size at the MP2/aug-cc-pVTZ level are also calculated for estimating the interaction energies at the complete basis set limit.     

Ab initio quality one-electron properties of large molecules: development and testing of molecular tailoring approach

The development of a linear-scaling method, viz. "molecular tailoring approach" with an emphasis on accurate computation of one-electron properties of large molecules is reported. This method is based on fragmenting the reference macromolecule into a number of small, overlapping molecules of similar size. The density matrix (DM) of the parent molecule is synthesized from the individual fragment DMs, computed separately at the Hartree-Fock (HF) level, and is used for property evaluation. In effect, this method reduces the O(N(3)) scaling order within HF theory to an n.O(N'(3)) one, where n is the number of fragments and N', the average number of basis functions in the fragment molecules. An algorithm and a program in FORTRAN 90 have been developed for an automated fragmentation of large molecular systems. One-electron properties such as the molecular electrostatic potential, molecular electron density along with their topography, as well as the dipole moment are computed using this approach for medium and large test chemical systems of varying nature (tocopherol, a model polypeptide and a silicious zeolite). The results are compared qualitatively and quantitatively with the corresponding actual ones for some cases. This method is also extended to obtain MP2 level DMs and electronic properties of large systems and found to be equally successful.     

WebMTA: a web-interface for ab initio geometry optimization of large molecules using molecular tailoring approach

A web-interface for geometry optimization of large molecules using a linear scaling method, i.e., cardinality guided molecular tailoring approach (CG-MTA), is presented. CG-MTA is a cut-and-stitch, fragmentation-based method developed in our laboratory, for linear scaling of conventional ab initio techniques. This interface provides limited access to CG-MTA-enabled GAMESS. It can be used to obtain fragmentation schemes for a given spatially extended molecule depending on the maximum allowed fragment size and minimum cut radius values provided by the user. Currently, we support submission of single point or geometry optimization jobs at Hartree-Fock and density functional theory levels of theory for systems containing between 80 to 200 first row atoms and comprising up to 1000 basis functions. The graphical user interface is built using HTML and Python at the back end. The back end farms out the jobs on an in-house Linux-based cluster running on Pentium-4 Class or higher machines using an @Home-based parallelization scheme (http://chem.unipune.ernet.in/ approximately tcg/mtaweb/).     

Free radical cyclization in molecular aggregates

The cyclization of free radicals has been investigated in micelles and multilamellar lipid bilayer vesicles. The substrate for cyclization is the amphipathic bromohydrin 7-bramo-octadec-11-ene-8-ol, 1. The radical is generated from 1 in aqueous micelles or vesicles by $\text{NaBH}{}_4\text{Bu}{}_3\text{SnCl}$. Four diastereomeric cyclopentanol products are formed in the 5-exo cyclization and the distribution of these products depends on the solvent and aggregate. Product distributions for cyclization in all media which have an aqueous/organic interface are significantly different from product distributions obtained for reactions in homogeneous media.     

两亲性分子聚集体的相变及其协同性

两亲性分子聚集体是一类重要的软物质,它们有着丰富而复杂的相行为.本文主要从两个方面综述了作者所在的研究组在两亲性分子聚集体相变研究方面的工作进展.(1)磷脂相关体系相变热力学:归纳了多种小分子(二甲基亚砜、甘油、海藻糖、尿素等)对于磷脂体系相行为的调控,比较并讨论了固醇类分子和葡萄糖神经酰胺分子诱导磷脂分子形成液态有序相的能力,还介绍了计算机模拟磷脂相行为的工作进展.(2)两亲性分子聚集体相变的协同性:先介绍了相变协同性(即分子头部、尾部、界面等基团在相变过程中的一致性)问题的提出,然后通过双十八烷基二甲基溴化铵分子和硬脂酰溶血卵磷脂两个体系的研究实例,说明两亲性分子聚集体相变过程中存在着头尾不一致的现象.对这个问题的研究,将为我们打开挑战相态转变的一系列重大问题(如相变动力学、相态多型性、相态稳定性以及相变可逆性等)的新窗口.     

Helical supramolecular nanorods via sequential meticulous tailoring of noncovalent interaction and light irradiation

Polymers are widely recognized to entail random conformations in good solvent governed by the need for achieving the highest entropy to reach thermodynamic equilibrium. In this context, it remains grand challenging to directly arrange them into ordered conformation as building blocks for further self-assembling into hierarchal structures. Herein, we report a simple yet viable strategy to progressively assemble rationally designed azobenzene-containing alternating copolymer(i.e., poly(binaphthyls...     

Probing the permeability of polyelectrolyte multilayer capsules via a molecular beacon approach

Application of polyelectrolyte multilayer (PEM) capsules as vehicles for the controlled delivery of substances, such as drugs, genes, pesticides, cosmetics, and foodstuffs, requires a sound understanding of the permeability of the capsules. We report the results of a detailed investigation into probing capsule permeability via a molecular beacon (MB) approach. This method involves preparing MB-functionalized bimodal mesoporous silica (BMSMB) particles, encapsulating the BMSMB particles within the PEM film to be probed, and then incubating the encapsulated BMSMB particles with DNA target sequences of different lengths. Permeation of the DNA targets through the capsule shell causes the immobilized MBs to open due to hybridization of the DNA targets with the complementary loop region of the MBs, resulting in an increase in the MB fluorescence. The assay conditions (BMSMB particle concentration, MB loading within the BMS particles, DNA target concentration, DNA target size, pH, sodium chloride concentration) where the MB-DNA sensing process is effective were first examined. The permeability of DNA through poly(sodium 4-styrenesulfonate) (PSS)/poly(allylamine hydrochloride) (PAH) multilayer films, with and without a poly(ethyleneimine) (PEI) precursor layer, was then investigated. The permeation of the DNA targets decreases considerably as the thickness of the PEM film encapsulating the BMSMB particles increases. Furthermore, the presence of a PEI precursor layer gives rise to less permeable PSS/PAH multilayers. The diffusion coefficients calculated for the DNA targets through the PEM capsules range from 10-19 to 10-18 m2 s-1. This investigation demonstrates that the MB approach to measuring permeability is an important new tool for the characterization of PEM capsules and is expected to be applicable for probing the permeability of other systems, such as membranes, liposomes, and emulsions.     

Characterizing quantum-sharing of electronic excitation in molecular aggregates

A key and long standing question regarding the function of photosynthetic systems concerns the advantages that delocalized electronic excitations and their coherent dynamics could offer to robust and efficient energy transfer within and between photosynthetic light-harvesting complexes. Here we discuss how the framework of entanglement can be used to characterize the strength and spatial distribution of electronic coherences in biomolecular aggregates, why this is interesting, and how one can go about investigating possible relations between non-vanishing electronic coherences and efficient excitation transfer from donors to acceptors. As an example we discuss how certain coherences may correlate to efficient energy transfer in the Fenna-Mathews-Olson complex. Perspectives about understanding advantages of coherence-assisted energy transfer are discussed.     

On the performance of molecular tailoring approach for estimation of the intramolecular hydrogen bond energies of RAHB systems: a comparative study

Structural Chemistry - In the current research, the performance of molecular tailoring approach (MTA) for estimation of the intramolecular hydrogen bond (IMHB) energies of the simple...     

Manipulating supramolecular self-assembly via tailoring pendant group size of linear vinyl polymers

In a series of poly[di(alkyl) vinylterephthalates] (PDAVTs) synthesized via radical polymerization, fine-tuning the size and shape of the side groups manipulated the supramolecular self-assembly and led to control over the formations between amorphous and 2D ordered hexagonal phases. To introduce the 2D long-range ordered structure, the size of the ester side groups at the 2- and 5-positions of the phenyl rings laterally attached to the backbones had to be in the range of propyl/isopropyl to hexyl. The relatively extended backbones observed in these polymers were attributed to steric effects from the side groups. When the n-alkyl groups were larger than hexyl, the ability to form the liquid crystalline phase gradually decreased. A completely disordered phase could be observed by substituting dodecyl groups as side groups.     

Stereochemical analysis of d-glucopyranosyl-sulfoxides via a combined NMR,molecular modeling and X-ray crystallographic approach

(S)-α-Methoxyphenylacetic acid (MPAA) was used as an NMR shift reagent in combination with molecular modeling to predict the absolute configuration of a representative epimeric pair of glucopyranosyl sulfoxides. The correctness of this assignment was confirmed by X-ray crystallographic examination of one of the epimers, 3a1. The crystal structure of ethyl 2,3-di-O-acetyl-4,6-O-benzylidene-1-thio-β-d-glucopyranoside S-oxide monohydrate 3a1 was solved by direct methods and was shown to bear the (R)-configuration at the sulfinyl center in accordance with our prediction. Furthermore, the conformation of 3a1 in the solid state was found to be remarkably similar to that predicted by molecular mechanics calculations.     

Theoretical methods for excited state dynamics of molecules and molecular aggregates

This contribution provides a summary of proposed theoretical and computational studies on excited state dynamics in molecular aggregates, as an important part of the National Natural Science Foundation (NNSF) Major Project entitled "Theoretical study of the low-lying electronic excited state for molecular aggregates". This study will focus on developments of novel methods to simulate excited state dynamics of molecular aggregates, with the aim of understanding several important chemical physics processes, and providing a solid foundation for predicting the opto-electronic properties of organic functional materials and devices. The contents of this study include: (1) The quantum chemical methods for electronic excited state and electronic couplings targeted for dynamics in molecular aggregates; (2) Methods to construct effective Hamiltonian models, and to solve their dynamics using system-bath approaches; (3) Non-adiabatic mixed quantum-classic methods targeted for molecular aggregates; (4) Theoretical studies of charge and energy transfer, and related spectroscopic phenomena in molecular aggregates.