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An overview of the use of classical mechanical molecular simulations of porphyrins, hydroporphyrins and heme proteins is given. The topics cover molecular mechanics calculations of structures and conformer energies of porphyrins, energies of barriers for interconversion between stable conformers, molecular dynamics of porphyrins and heme proteins, and normal-coordinate structural analysis of experimental and calculated porphyrin structures. Molecular mechanics and dynamics are currently a fertile area of research on porphyrins. In the future, other computational methods such as Monte Carlo simulations, which have yet to be applied to porphyrins, will come into use and open new avenues of research into molecular simulations of porphyrins.

In this paper, a novel astrophysics-based prediction framework is developed for estimating the binding affinity of a glucose binder. The proposed framework utilizes the molecule properties for predicting the binding affinity. It also uses the astrophysics-learning strategy that incorporates the concepts of Kepler’s law during the prediction process. The proposed framework is compared with 10 regression algorithms over ZINC dataset. Experimental results reveal that the proposed framework provides 99.30% accuracy of predicting binding affinity. However, decision tree provides the prediction with 97.14% accuracy. Cross-validation results show that the proposed framework provides better accuracy than the other existing models. The developed framework enables researchers to screen glucose binder rapidly. It also reduces computational time for designing small glucose binding molecule.

Using N-Methylacetamide (NMA) dimer and NMA–water as model complexes, the solvent effect on the protein inter- N–H⋯O=C and intra- N –H⋯OH₂, and C=O⋯H₂O hydrogen bonding have been studied by the polarizable continuum model (PCM) ab initio calculations in the four media (vacuum, ether, nitromethane and water). In contrast to the empirical approaches, we suggested using the direction interaction energies (DE) to consider the solvent polarization, which can be derived from PCM ab initio calculations. The DEs of the model compounds in solvents are larger than their in vacuo binding energies, which reflect the solvent polarization effect. As the solvents become increasingly polar, the binding free energies decrease while DEs increase. The increasing DE is consistent with the increasing hydrogen bond length. Considering the protein environment, the DEs of NMA-NMA dimer in ether, 9.14 and 9.41 kcal/mol for NMADI and NMADII, are recommended for the intra N–H⋯O=C hydrogen bonding. The DEs of NMA–water complex in water, -5.47 (NMAWI) and -5.41 kcal/mol (NMAWI'), -8.44 (NMAWII) and -8.68 kcal/mol (NMAWII'), respectively, are suggested for the inter- N–H⋯OH₂ and C–O⋯H₂O hydrogen bonding of proteins. Using the same approach, we have also computed the DE of water dimer in liquid water. The computed DE of water dimer (-5.63 kcal/mol) is larger than the in vacuo water dimerization energy (-5.14 kcal/mol) and in reasonable agreement with the dimerization energies (ranging from –6.0 to 6.8 kcal/mol) of polarization-included empirical water models.

Molecular mechanics (MM) method followed by molecular dynamics (MD) simulation was carried out to investigate the stability of an aggregate formed by self-assembling of peptide amphiphile (PA) molecules. The MM + MD simulation confirms that the cylindrical shaped aggregate is very stable. The analysis showed that the remarkable stability of the aggregate was partly due to various intermolecular hydrogen-bond interactions between polar groups of PA molecules. The hydrophobic alkyl tails of PA molecules are packed loosely inside the interior of the aggregates. The packing of alkyl tails contribute further stability of the PA aggregate. Our simulations reproduce qualitatively experimental observations and support the fact that PA molecules are self-assembled within closed intermolecular distance to favor the forming of disulfide bonds.

The urea inclusion compounds, a unique polar organic crystalline complex, are considered as a potential candidate for a molecular separator of long chain alkane molecule. A well-defined structure of the crystalline channel systems constructed from hydrogen bonding arrangement of the urea molecules, can be used to understand the fundamental aspects of the processes involving ions or molecules transportation. To do so, in our work, molecular dynamics approach is implemented to understand the behavioral pattern of the hexadecane-1,16-diol and hexadecane guests’ related to translational and rotational orientation along the urea tunnel. Our obtained results reveal that high interaction of hexadecane-1,16-diol with urea host molecules offers a restricted environment inside urea tunnel, resulting in slowing down the guest movement. Hexadecane guest system, on the contrary, exhibits lower interaction whereby the translational and rotational movement is faster. Moreover, as the distance increases (along $c$-axis) in the urea tunnel, both guest systems favor a clockwise rotational orientation. Preference of the respected orientation indicates the influence of chiral urea tunnel on achiral guests that is clathrate inside the tunnel structure.

Sterically bulky substituents at the β-carbons of the pyrrole rings of porphyrins are sufficient to cause large out-of-plane porphyrin distortions even in the absence of substituent groups at the meso carbons. It is well established that substituents at the meso-positions only or at both the β-pyrrole and the meso-positions are sufficiently bulky to result in large non-planar distortions of the macrocycle. However, no systematic studies of the effects of bulky β-pyrrole substituents alone have been reported. Herein, molecular simulations and X-ray crystallography of nickel(II) 2,3,7,8,12,13,17,18-octa(isopropyl)porphyrin reveal that large out-of-plane distortions (>1.5 Å) are induced by the steric repulsion of the β-isopropyl groups but fail to lead to a single strongly energetically favored conformer. The molecular simulations indicate that multiple conformers differing in the orientation of the isopropyl groups and the macrocycle conformation coexist in solution and this is confirmed by resonance Raman spectroscopy. Large downshifts in the structure-sensitive lines result from the non-planar distortion, and line broadenings result from structural heterogeneity. The heterogeneity originates from tradeoffs between energy contributions from steric repulsion and macrocycle distortion. Simulations for 5-nitro-2,3,7,8,12,13,17,18-octa(isopropyl)porphyrin suggest two possible orientations of the nitro group with respect to the macrocycle mean plane — one nearly vertical (as in the crystal structure) and another that is nearly parallel. INDO/S semiempirical calculations indicate an orbital of the NO₂ group resides between the porphyrin frontier orbitals with significant mixing of the nitro and porphyrin orbitals.KEYWORDS: porphyrin, non-planar, resonance Raman, X-ray crystallography, crystal structure, isopropyl, nitro, conformer, molecular mechanics, molecular simulations, density functional theory, steric crowding, conformational heterogeneity.

Cyclic voltammetry and thin-layer spectroelectrochemical properties of the free base 5,10,15,20-tetrakis(1,3-benzodioxole)porphyrin (H₂P), and its manganese and iron complexes (MnP and FeP, respectively) were studied in dichloromethane with tetra-butyl ammonium hexafluorophosphate (TBAPF₆) as supporting electrolyte. The free base undergoes two monoelectronic oxidations at +0.71 and +0.96 V vs. Ag/Ag⁺, corresponding to the formations of the π-cation radical and dication. Two reductions were observed at -1.53 and -1.87 V corresponding to the formation of π-anion and dianion species. The cyclic voltammograms of the Mn^III and Fe^III complexes also showed a reversible process centered in the metal ion with E_1/2 values at -0.61 and -0.59 V, respectively. In a typical experiment, in situ spectroelectrochemical response showed a decrease of the Soret band at 422 nm, a red shift of the Q-bands, and the new low intensity bands between 800–950 nm range. Structural features and spectroscopic assignments were proposed and discussed based on semi-empirical (molecular mechanics MMFF and ZINDO/S (Zerner method of intermediate neglect of differential overlap for spectroscopy) calculations.

Single-molecule mechanics of DNA/RNA, polypeptide and protein has become a new frontier in life sciences. There is an increasing need in participant of researcher in applied mechanics to perform a systematic study on methodologies and basic sciences in molecular mechanics. The wide-applied continuum mechanics may not be applicable in study of the biomolecules. At the same time, the all-atom molecular dynamics method is severely limited by the size and time scales of systems it can simulate. As an alternative, coarse-grained models have recently enjoyed intense interest. Coarse-grained representations combined with enhanced computer power currently allow the simulation of systems of biologically relevant size (submicrometric) and timescale (microsecond or millisecond). In this paper, we reported some progresses we made in the modeling of biomolecules using the coarse-grained methods including, the collapse of biopolymers, the dynamics of HIV-1 protease and the binding dynamics of inhibitors into the protease, aiming to stimulating a broader interest in developing molecular mechanics.

The unique lattice structure and properties of graphene have drawn tremendous interests recently. By combining continuum and atomistic approaches, this paper investigates the mechanical properties of single-atomic-layer graphene sheets. A theoretical framework of nonlinear continuum mechanics is developed for graphene under both in-plane and bending deformation. Atomistic simulations are carried out to deduce the effective mechanical properties. It is found that graphene becomes highly nonlinear and anisotropic under finite-strain uniaxial stretch, and coupling between stretch and shear occurs except for stretching in the zigzag and armchair directions. The theoretical strength (fracture strain and fracture stress) of perfect graphene lattice also varies with the chiral direction of uniaxial stretch. By rolling graphene sheets into cylindrical tubes of various radii, the bending modulus of graphene is obtained. Buckling of graphene ribbons under uniaxial compression is simulated and the critical strain for the onset of buckling is compared to a linear buckling analysis.

Folding in graphene sheet has been extensively observed experimentally. While it is generally recognized that such a conformational state can influence the electronic, magnetic and mechanical properties of graphene nanostructures, the mechanism driving the nonlinear mechanical deformation remains an interesting subject of study. Here we present an investigation on the folding in bi-layer graphene sheet due to in-plane compression. To describe the lattice registry effect of interlay cohesion in layered graphitic structures, a registry-dependent potential model was implemented. We have determined the critical length to stabilize the graphene folding to be 5.4~10.7 nm through both theoretical and simulation analysis. The mechanism for such a stabilized fold is attributed to the variations in the inter-layer interaction energy that produces a friction-like effect. The climbing image nudged elastic band (CINEB) calculations predicted an identical activation energy barrier associated with the transition between flat and folded configurations, 0.47 eV/Å, for graphene sheets with length of 7~10 nm. When the mechanical stimulation is high enough to overcome the energy barrier, the supported graphene sheet can be folded to form a nanotube.

Possessing exceptional properties, graphene has garnered immense interest in the research community for a wide array of potential applications. The mechanical properties play an important role in the success of the potential applications and thus a thorough understanding is cardinal. Computational modeling and simulation is an important tool in the design process due to the low costs compared to the experimental means. This review aims to consolidate the findings of works of computational modeling and simulation of graphene, with focus on models at the continuum and molecular levels. The review shows intrinsic differences in focus of the applications and types of graphene investigated by the different scale models, thus highlighting the advantages and shortcomings of each type of modeling approach.

The nature of diamond–graphite hybrids has been studied by molecular mechanics, by examining the structures of species such as C₈₄H_x wherein the sp³ to sp² carbon ratio is varied progressively. The dependence of the average coordination number on the atom fraction of hydrogen has been examined in the light of the random covalent network model. The HOMO–LUMO gap has been estimated in a graphite-like C₁₁₀H_x and in a diamond-like C₁₂₀H_x as a function of the sp³/sp² carbon atom ratio. The gap increases exponentially with the fraction of sp³ carbon. Shapes of fullerene-like structures with 7-membered rings, in addition to 6- and 5-membered rings, have been investigated along with structures of bent nanotubes having similar ring systems.

Facile and co-operative 2D syntheses of new functionals (E)-1-(3-chloro-4-(alkoxy)-phenyl)-2-phenyl-diazene and their stoichiometrically ordered assembly of parallel-stacked unit mixed-H type aggregates as building blocks are described upon neat addition of charged fluorescent units of Rh B to the interfacial photochromes. For these integrated assemblies, molecular order was encoded in the shape and chemical functionality and was governed by the strength and directionality of secondary interactions. The solution phase H- type aggregates from the amphiphiles required long range orientational order; transformation into more stable tubular architectures with controlled molecular alignment at 2D was energetically favorable solely on account of surface-induced phenomena. Rh B influenced π–π interaction and anisotropic polarizability in addition to electronic interactions, while the diazene derivatives supported coulombic binding.

For the same amphiphiles to form J aggregates, a two component interfacial matrix stabilization technique was necessitated and devised. Langmuir isotherms of (E)-1-(3-chloro-4-(alkyloxy)phenyl)-2-phenyldiazene (C_nCD, n = 8, 10, 12) with stearic acid (STA) as the two dimensional matrix revealed a phase separation of the C_nCD from the matrix at a compression pressure of 10 mN/m. While a one component C_nCD failed to form a 2D monolayer, the STA supported C_nCD binary system crossed a compression induced mixed monolayer phase with formation of highly ordered matrix stabilized and phase separated C_nCDJ-aggregate upon proper tuning of STA- CnCD ratio, suggesting a 'know-how' for the preparation of J-aggregates from hydrophobic functionals.

The dimeric association of a Fullerene (C₆₀)-N,N-dimethylaminoazobenzene dyad (DPNME), a donor-bridge-acceptor hybrid has been explored. The study started by presenting a comprehensive DFT-study on the dyad, continued by investigation of its tunable self assembly as a function of solvent polarity in a more exploratory manner and finished with an extensive discussion on its dimerization, where the electronic coupling of the azo chromophore with the substituted 3D Fullerene C₆₀ had a predominant impact on the structure organization. For a binary solvent dielectric constant 7.56 ≤ ε ≤ 66, a solvent polarity dependent dynamic equilibrium between the monomer ⅉ J-aggregate ↔ H-aggregate was established. A synergetic effect of the intermolecular donor-acceptor interaction between the electron deficient fullerene ring and the electron rich N,N-dimethylamino substituted aromatic ring governed the process of aggregation with predominant van der Waals and π-π interaction between a pair of dimers. The linear geometry of the donor and the conformational rigidity of the Fullerene C₆₀ acceptor played crucial roles in envisaging the resulting π-extended network. An important part of the work comprised of our emphasis on the observed finite oscillator strength of the hitherto forbidden anti-parallel H-aggregates. The results established a novel chromophoric system in fullerene (C₆₀)- azobenzene hybrid for the construction of supramolecular assemblies with opto-electronically active constituents. Importantly, substitution of fullerene C₆₀ with the J-aggregate forming AZNME chromophore yielded the anti-parallel H-dimer. The overall process of H and J aggregate formation represented significant advance towards controlled molecular self assembly with predictable shapes by controlling the surface molecular density and bulk phase chemical structure and solvent polarity. The results exposed interesting new model systems for dye aggregates from which laws of cluster formation could be deduced and the ability to organize the building blocks in a specified direction could provide insight for nano-electronics design.