Noncovalent Interactions of DNA Bases with Naphthalene and Graphene

Regulation of transmembrane current through modulation of biomimetic lipid membrane composition

Ion transport through biological channels is influenced not only by the structural properties of the channels themselves but also by the composition of the phospholipid membrane, which acts as a scaffold for these nanochannels. Drawing inspiration from how lipid membrane composition modulates ion currents, as seen in the activation of the K+ channel in Streptomyces A (KcsA) by anionic lipids, we propose a biomimetic nanochannel system that integrates DNA nanotechnology with two-dimensional graphene oxide (GO) nanosheets. By modifying the length of the multibranched DNA nanowires generated through the hybridization chain reaction (HCR) and varying the concentration of the linker strands that integrate these DNA nanowire structures with the GO membrane, the composition of the membrane can be effectively adjusted, consequently impacting ion transport. This method provides a strategy for developing devices with highly efficient and tunable ion transport, suitable for applications in mass transport, environmental protection, biomimetic channels, and biosensors.

Precise control of transmembrane current via regulating bionic lipid membrane composition

The transport of ions through biological ion channels is regulated not only by their structural characteristics but also by the composition of the phospholipid membrane, which serves as a carrier for nanochannels. Inspired by the modulation of ion currents by lipid membrane composition, exemplified by the activation of the K+ channel of Streptomyces A by anionic lipids, we present a biomimetic nanochannel system based on combining DNA nanotechnology with two-dimensional graphene oxide (GO) nanosheets. By designing multibranched DNA nanowires, we assemble programmable DNA scaffold networks (DSNs) on the GO surface to precisely control membrane composition. Modulating the DSN layers from one to five enhances DNA composition, yielding a maximum 12-fold enhancement in ion current, primarily due to charge effects. Incorporating DNAzymes facilitates reversible modulation of membrane composition, enabling cyclic conversion of ion current. This approach offers a pathway for creating devices with highly efficient, tunable ion transport, applicable in diverse fields like mass transport, environmental protection, biomimetic channels, and biosensors.

A dual-targeting antifungal is effective against multidrug-resistant human fungal pathogens

Drug-resistant fungal infections pose a significant threat to human health. Dual-targeting compounds, which have multiple targets on a single pathogen, offer an effective approach to combat drug-resistant pathogens, although ensuring potent activity and high selectivity remains a challenge. Here we propose a dual-targeting strategy for designing antifungal compounds. We incorporate DNA-binding naphthalene groups as the hydrophobic moieties into the host defence peptide-mimicking poly(2-oxazoline)s. This resulted in a compound, (Gly0.8Nap0.2)20, which targets both the fungal membrane and DNA. This compound kills clinical strains of multidrug-resistant fungi including Candida spp., Cryptococcus neoformans, Cryptococcus gattii and Aspergillus fumigatus. (Gly0.8Nap0.2)20 shows superior performance compared with amphotericin B by showing not only potent antifungal activities but also high antifungal selectivity. The compound also does not induce antimicrobial resistance. Moreover, (Gly0.8Nap0.2)20 exhibits promising in vivo therapeutic activities against drug-resistant Candida albicans in mouse models of skin abrasion, corneal infection and systemic infection. This study shows that dual-targeting antifungal compounds may be effective in combating drug-resistant fungal pathogens and mitigating fungal resistance.

Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials

Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.

Ab Initio investigation for DNA nucleotide bases sequencing using chiral carbon nanobelts and nanotubes

Understanding the interaction mechanism between DNA nucleotide bases and carbon nanomaterials is an important issue in the field of identifying nucleotide molecules sequencing. In this article, the adsorption behavior of DNA nucleotide bases on the external surface of chiral carbon nanobelts (CNBs) (6, 5), (7, 6) and (8, 6), was comprehensively investigated from electronic and optical perspectives. As a result, it was determined that the DNA nucleotide bases have optical absorption in the ultraviolet region. When bases are adsorbed on the surface of CNBs, the optical absorption peak of the new complex structure shifted to the visible region. The study of the optical properties of selected CNBs showed that CNB (6,5) performs better in detecting Cytosine and the red shift in the absorption spectrum of complex structure is noticeable. Also, the effect of infinite length for chiral CNTs in DNA nucleotide base sequencing was investigated using DFTB approach. Our investigations based on electronic properties showed that CNTs have better performance than CNBs in DNA nucleotide base sequencing.

Graphene Oxide Nanostructures as Nanoplatforms for Delivering Natural Therapeutic Agents: Applications in Cancer Treatment, Bacterial Infections, and Bone Regeneration Medicine

Graphene, fullerenes, diamond, carbon nanotubes, and carbon dots are just a few of the carbon-based nanomaterials that have gained enormous popularity in a variety of scientific disciplines and industrial uses. As a two-dimensional material in the creation of therapeutic delivery systems for many illnesses, nanosized graphene oxide (NGO) is now garnering a large amount of attention among these materials. In addition to other benefits, NGO functions as a drug nanocarrier with remarkable biocompatibility, high pharmaceutical loading capacity, controlled drug release capability, biological imaging efficiency, multifunctional nanoplatform properties, and the power to increase the therapeutic efficacy of loaded agents. Thus, NGO is a perfect nanoplatform for the development of drug delivery systems (DDSs) to both detect and treat a variety of ailments. This review article's main focus is on investigating surface functionality, drug-loading methods, and drug release patterns designed particularly for smart delivery systems. The paper also examines the relevance of using NGOs to build DDSs and considers prospective uses in the treatment of diseases including cancer, infection by bacteria, and bone regeneration medicine. These factors cover the use of naturally occurring medicinal substances produced from plant-based sources.

Review of research of nanocomposites based on graphene quantum dots

Graphene quantum dots (GQDs) belong to the vast and versatile family of carbon nanomaterials. Their unique position amongst versatile carbon nanoparticles (NPs) originates from the properties of quantum confinement and edge effects. GQDs are similar to conventional semiconductor QDs due to their tunable band gaps and high photoluminescence activity. However, GQDs have superior characteristics due to their excellent biocompatibility, low toxicity, good water dispersibility, large optical absorptivity, high fluorescence activity and photostability. These properties have generated significant interest in GQDs applications in various fields: nanosensor fabrication, drug delivery, photocatalysis, photovoltaics, and photodynamic therapy. Numerous GQD-based nanocomposites/nanohybrides have been synthesized and/or studied computationally. This review focuses on recent computational studies of various GQD-based nanocomposites/nanohybrides and systems which can be related to them.

Facile room-temperature self-assembly of extended cation-free guanine-quartet network on Mo-doped Au(111) surface

Guanine-quadruplex, consisting of several stacked guanine-quartets (GQs), has emerged as an important category of novel molecular targets with applications from nanoelectronic devices to anticancer drugs. Incorporation of metal cations into a GQ structure is utilized to form stable G-quadruplexes, while formation of a cation-free GQ network has been challenging. Here we report the room temperature (RT) molecular self-assembly of extended pristine GQ networks on an Au(111) surface. An implanted molybdenum atom within the Au(111) surface is used to nucleate and stabilize the cation-free GQ network. Additionally, decoration of the Au(111) surface with 7-armchair graphene nanoribbons (7-AGNRs) enhances the GQ domain size by suppressing the influence of the disordered phase nucleated from Au step edges. Scanning tunneling microscopy/spectroscopy (STM/STS) and density functional theory (DFT) calculations confirm the formation of GQ networks and unravel the nucleation and growth mechanism. Our work, utilizing a hetero-atom doped substrate, provides a facile approach to enhance the stability and domain size of the GQ self-assembly, which would be applicable for other molecular structures.

e-Graphene: A Computational Platform for the Prediction of Graphene-Based Drug Delivery System by Quantum Genetic Algorithm and Cascade Protocol

Graphene, as a novel category of carbon nanomaterials, has attracted a great attention in the field of drug delivery. Due to its large dual surface area, graphene can efficiently load drug molecules with high capacity via non-covalent interaction without chemical modification of the drugs. Hence, it ignites prevalent interests in developing a new graphene/graphene oxide (GO)-based drug delivery system (GDDS). However, current design of GDDS primarily depends on the prior experimental experience with the trial-and-error method. Thus, it is more appealing to theoretically predict possible GDDS candidates before experiments. Toward this end, we propose to fuse quantum genetic algorithm (QGA) and quantum mechanics (QM)/semi-empirical quantum mechanics (SQM)/force field (FF) to globally search the optimal binding interaction between the graphene/GO and drug in a given GDDS and develop a free computational platform “e-Graphene” to automatically predict/screen potential GDDS candidates. To make this platform more pragmatic for the rapid yet relatively accurate prediction, we further propose a cascade protocol via firstly conducting a fast QGA/FF calculation with fine QGA parameters and automatically passing the best chromosomes from QGA/FF to initialize a higher level QGA/SQM or QGA/QM calculation with coarse QGA parameters (e.g., small populations and short evolution generations). By harnessing this platform and protocol, systematic tests on a typical GDDS containing an anticancer drug SN38 illustrate that high fabrication rates of hydroxyl, epoxy, and carboxyl groups on a pristine graphene model will compromise the stability of GDDS, implying that an appropriate functionalization rate is crucial for the delicate balance between the stability and solubility/biocompatibility of GDDS. Moreover, automatic GDDS screen in the DrugBank database is performed and elicits four potential GDDS candidates with enhanced stability than the commonly tested GDDS containing SN38 from the computational point of view. We hope that this work can provide a useful program and protocol for experimental scientists to rationally design/screen promising GDDS candidates prior to experimental tests.

Docking and molecular dynamics predicted B-DNA and dihydropyrimidinone selenoesters interactions elucidating antiproliferative effects on breast adenocarcinoma cells

Dihydropyrimidinones have demonstrated different biological activities including anticancer properties. Cytotoxic potential and antiproliferative potential of new dihydropyrimidinone-derived selenoesters (Se-DHPM) compounds were assessed in vitro against the breast adenocarcinoma cells (MCF-7). Among the eight Se-DHPM compounds tested just 49A and 49F were the most cytotoxic for MCF-7 and the most selective for the non-tumor strain (McCoy) and reduced cell viability in a time- and concentration-dependent manner. Compounds 49A and 49F increased the rate of cell death due to apoptosis and necrosis comparatively to the control, however only the 49F showed antiproliferative potential, reducing the number of colonies formed. In the molecular assay 49A interacts with CT-DNA and caused hyperchromism while 49F caused a hypochromic effect. The intercalation test revealed that the two compounds caused destabilization in the CT-DNA molecule. This effect was evidenced by the loss of fluorescence when the compounds competed and caused the displacement of propidium iodide. Simulations (docking and molecular dynamics) using B-DNA brought a greater understanding of ligand-B-DNA interactions. Furthermore, they predicted that the compounds act as minor groove ligands that are stabilized through hydrogen bonds and hydrophobic interactions. However, the form of interaction foreseen for 49A was more energetically favorable and had more stable hydrogen bonds during the simulation time. Despite some violations foreseen in the ADMET for 49F, the set of other results point to this Se-DHPM as a promising leader compound with anti-tumor potential for breast cancer.Communicated by Ramaswamy H. Sarma.

Polarization influences the evolution of nucleobase-graphene interactions

In recent years, graphene has attracted attention from researchers as an atomistically thin solid state material for the study on the self-assembly of nucleobases. Non-covalent interactions between nucleobases and graphene sheets play a fundamental role in understanding the self-assembly of nucleobases on the graphene sheet. A fundamental understanding of the effect of molecular polarizability on these non-covalent interactions between the nucleobases and the underlying graphene sheet is absent in the literature. In this paper, we present the results from polarizable molecular dynamics simulation studies to understand the effect of polarization on the strength of non-covalent interactions. To this end, we report the development of Drude parameters for describing the polarizable graphene sheet. The developed parameters were used to study the self-aggregation phenomenon of nucleobases on a graphene support. We observe a significant change in the interaction patterns upon the inclusion of polarization into the system, with polarizable simulations yielding results that closely resemble the experimental studies. Two of the key observations were the probability of the formation of stacks in guanine-rich systems, and the spontaneous formation of H-bonded structures over the graphene sheet, which allude to the importance of the DNA sequence and composition. Both these effects were not observed in the additive simulations. The present study sheds light on the effect of polarization on the adsorption of DNA nucleobases on a graphene sheet, but the methodology can be extended to include a variety of small molecules and complete DNA strands.

Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics

This work deals with first-principles and in silico studies of graphene oxide-based whole-cell selective aptamers for cancer diagnostics utilising a tunable-surface strategy. Herein, graphene oxide (GO) was constructed as a surface-based model with poly(N-isopropylacrylamide) (PNIPAM) covalently grafted as an "on/off"-switch in triggering interactions with the cancer-cell protein around its lower critical solution temperature. The atomic building blocks of the aptamer and the PNIPAM adsorbed onto the GO was investigated at the density functional theory (DFT) level. The presence of the monomer of PNIPAM stabilised the system's π-π interaction between GO and its nucleobases as confirmed by higher bandgap energy, satisfying the eigenvalues of the single-point energy observed rather than the nucleobase and the GO complex independently. The unaltered geometrical structures of the surface emphasise the physisorption type interaction between the nucleobase and the GO/NIPAM surface. The docking result for the aptamer and the protein, highlighted the behavior of the PNIPAM-graft-GO  is exhibiting globular and extended conformations, further supported by molecular dynamics (MD) simulations. These studies enabled a better understanding of the thermal responsive behavior of the polymer-enhanced GO complex for whole-cell protein interactions through computational methods.

Understanding the non-covalent interaction mediated modulations on the electronic structure of quasi-zero-dimensional graphene nanoflakes

In recent years, magnetic or electric field induced modulations on the electronic environment of single molecular systems are common practice. In this particular study, we have instigated the possibility of controlling the electronic and spin-dependent properties of hydrogen-terminated graphene fragments, so-called graphene nanoflakes (GNF), using weak non-covalent interactions as the external stimuli. The topological frustration in the graphene fragment appreciated the compelling electronic behavior of the system. This leads to some unorthodox spin-distribution in the system and it is possible to synchronize this electronic perturbation switching through a non-covalent interaction. These findings institute a new avenue for sculpting such donor-acceptor composites as self-regulated spintronic devices in next generation electronics.

Combined molecular and periodic DFT analysis of the adsorption of co macrocycles on graphene

The molecular doping of graphene with π-stacked conjugated molecules has been widely studied during the last 10 years, both experimentally or using first-principle calculations, mainly with strongly acceptor or donor molecules. Macrocyclic metal complexes have been far less studied and their behavior on graphene is less clear-cut. The present density functional theory study of cobalt porphyrin and phthalocyanine adsorbed on monolayer or bilayer graphene allows to compare the outcomes of two models, either a finite-sized flake of graphene or an infinite 2D material using periodic calculations. The electronic structures yielded by both models are compared, with a focus on the density of states around the Fermi level. Apart from the crucial choice of calculation conditions, this investigation also shows that unlike strongly donating or accepting organic dopants, these macrocycles do not induce a significant doping of the graphene sheet and that a finite size model of graphene flake may be confidently used for most modeling purposes. © 2017 Wiley Periodicals, Inc.

Pd nanoparticles immobilized on carbon nanotubes with a polyaniline coaxial coating for the Heck reaction: coating thickness as the key factor influencing the efficiency and stability of the catalyst

Pd/PANI@CNTs were synthesized using a low-cost and simple method. The thickness of the PANI layer is the key in determining the stability of the catalyst in the Heck reaction.

Stick-Slip Motion of ssDNA over Graphene

We have performed molecular dynamics simulations of nanomanipulation experiments on short single-stranded DNA chains elastically driven on a graphene surface. After a brief transient, reproducible stick-slip cycles are observed on chains made by 10 units of thymine, cytosine, adenine, and guanine. The cycles have the periodicity of the graphene substrate, and take place via an intermediate stage, appearing as a dip in the sawtooth variations of lateral force recorded while the chains are manipulated. Guanine presents remarkable differences from the other bases, since a lower number of nucleotides are prone to stick to the substrate in this case. Nevertheless, the magnitudes of static friction and lateral stiffness are similar for all chains (30 pN and 0.7 N/m per adsorbed nucleotide respectively).

Noncovalent Interaction of Graphene with Heterocyclic Compounds: Benzene, Imidazole, Tetracene, and Imidazophenazines

Noncovalent functionalization of graphene with organic molecules offers a direct route to multifunctional modification of this nanomaterial, leading to its various possible practical applications. In this work, the structures of hybrids formed by linear heterocyclic compounds such as imidazophenazine (F1) and its derivatives (F2-F4) with graphene and the corresponding interaction energies are studied by using the DFT method. Special attention is paid to the hybrids where the attached molecule is located along the graphene zigzag (GZZ ) and armchair (GAC ) directions. The interaction energies corresponding to the graphene hybrids of the F1-F4 compounds for the two directions are found to be distinct, while tetracene (being a symmetrical molecule) shows a small difference between these binding energies. It is found that the back-side CH3 and CF3 groups have an important influence on the arrangements of F1 derivatives on graphene and on their binding energies. The contribution of the CF3 group to the total binding energy of the F3 molecule with graphene is the largest (3.4 kcal mol(-1) ) (the GZZ direction) while the CH3 group increases this energy of F2 only by 2.0 kcal mol(-1) (the GAC direction). It is shown that replacing the carbons with other atoms or adding a back-side group enables one to vary the polarizability of graphene.

Theoretical study of chlordecone and surface groups interaction in an activated carbon model under acidic and neutral conditions

Activated carbons (ACs) are widely used in the purification of drinking water without almost any knowledge about the adsorption mechanisms of the persistent organic pollutants. Chlordecone (CLD, Kepone) is an organochlorinated synthetic compound that has been used mainly as agricultural insecticide. CLD has been identified and listed as a persistent organic pollutant by the Stockholm Convention. The selection of the best suited AC for this type of contaminants is mainly an empirical and costly process. A theoretical study of the influence of AC surface groups (SGs) on CLD adsorption is done in order to help understanding the process. This may provide a first selection criteria for the preparation of AC with suitable surface properties. A model of AC consisting of a seven membered ring graphene sheet (coronene) with a functional group on the edge was used to evaluate the influence of the SGs over the adsorption. Multiple Minima Hypersurface methodology (MMH) coupled with PM7 semiempirical Hamiltonian was employed in order to study the interactions of the chlordecone with SGs (hydroxyl and carboxyl) at acidic and neutral pH and different hydration conditions. Selected structures were re-optimized using CAM-B3LYP to achieve a well-defined electron density to characterize the interactions by the Quantum Theory of Atoms in Molecules approach. The deprotonated form of surface carboxyl and hydroxyl groups of AC models show the strongest interactions, suggesting a chemical adsorption. An increase in carboxylic SGs content is proposed to enhance CLD adsorption onto AC at neutral pH conditions.

Modelling of graphene functionalization

This perspective describes the available theoretical methods and models for simulating graphene functionalization based on quantum and classical mechanics.

Electrostatics of DNA nucleotide-carbon nanotube hybrids evaluated from QM:MM simulations

Biomolecule-functionalized carbon nanotubes (CNTs) have been studied vastly in recent years due to their potential applications for instance in cancer detection, purification and separation of CNTs, and nanoelectronics. Studying the electrostatic potential generated by a biomolecule-CNT hybrid is important in predicting its interactions with the surrounding environment such as charged particles and surfaces. In this paper, we performed atomistic simulations using a QM:MM approach to evaluate the electrostatic potential and charge transfer for a hybrid structure formed by a DNA nucleotide and a CNT in solution. Four types of DNA nucleotides and two CNTs with chiralities of (4,4) and (7,0) were considered. The types of nucleotides and CNTs were both found to play important roles in the electrostatic potential and charge transfer of the hybrid. At the same distance from the CNT axis, the electrostatic potential for the nucleotide-(4,4) CNT hybrids was found to be stronger compared with that for the nucleotide-(7,0) CNT hybrids. Higher electric charge was also shown to be transferred from the DNA nucleotides to the (7,0) CNT compared with the (4,4) CNT. These results correlate with the previous finding that the nucleotides bound more tightly to the (7,0) CNT compared with the (4,4) CNT.

A QM:MM model for the interaction of DNA nucleotides with carbon nanotubes

Hybrid materials formed by DNA and carbon nanotubes (CNTs) have shown very interesting properties, but their simulation in solution using quantum mechanical approaches is still a challenge in the computational chemistry community. In this paper, we developed a QM:MM model to study the interactions between charged DNA nucleotides and carbon nanotubes in solution. All four types of DNA nucleotides were taken to interact with two CNTs of similar diameter but different chiralities: (4,4) and (7,0). The nucleotides and CNTs were treated at the QM level, while added water and neutralizing ions were modeled at the MM level. ONIOM simulations were performed at the (M06-2X/6-31G(d):Amber) level for the hybrids, as well as for individually solvated CNTs and nucleotides, which allowed us to evaluate the energy of binding. Our binding energy (BE) values range from 146.60 to 503.43 kJ mol(-1), indicating strong physisorption of nucleotides on CNTs. The relatively large BE, compared with past studies on nucleobase-CNT binding in a vacuum, could be due to the larger size of nucleotides compared with nucleobases, the charges on the nucleotides, and the inclusion of solution which causes the release of water molecules upon hybridization.

Benchmark calculations of the adsorption of aromatic molecules on graphene

Selecting the saturated graphene fragment as a model of graphene, we have investigated seven popular density functionals, including ωB97X-D, B97-D, B-LYP-D3, M05-2X, M06-2X, M11-L, and N12, for their performance in describing the adsorption of aromatic molecules on graphene. The best performing functionals are B97-D, B-LYP-D3, and ωB97X-D. M05-2X, M06-2X, and M11-L significantly underestimate the adsorption strengths, while N12 fails completely in this respect. The effects of the basis sets and size of the saturated graphene fragments on the geometries, energies, and properties for the adsorption of aromatic molecules on graphene have also been studied. It was found that the small basis sets such as 6-31G(d) and jun-cc-pVDZ are not suitable for the accurate description of the adsorption of aromatic molecules on graphene. The size of selected graphene fragments has a little effect on both the ωB97X-D and SCS-SAPT0 interaction energies, but the effects of the size of selected graphene fragments on the energy components are significant in some cases of the adsorption of aromatic molecules on graphene. The surprising weakness of electrostatic interactions by F substitution for the adsorption of F-substituted benzenes on graphene was explained using the energy component analysis.

Substituent Effects in π-Stacking of Histidine on Functionalized-SWNT and Graphene

Adsorptions of histidine on the functionalized (10,0) single-walled carbon nanotube (SWNT) and graphene were investigated using density function theory methods, M05-2x and DFT-D. The results show that the binding of the histidine ring to the functionalized SWNT is weaker than that to the pristine SWNT for both singlet and triplet complexes, regardless of the electron-donating (-OH, -NH₂) or electron-withdrawing (-COOH) character and their attached sites. The present decreased binding is opposite to the well-known enhanced binding in the substituted benzene dimers. Since the atoms of the histidine are distant from the substituent atoms by over 6Å, there would be no direct interaction between histidine and the substituent as in the case of the substituted benzene systems. The decreased binding can be mainly driven by the aromaticity of the functionalized SWNT. The nucleus-independent chemical shift (NICS) index analysis for the functionalized SWNTs in deed shows that local aromaticity of SWNT is decreased because of the electron redistribution induced by functional groups, and the π-π stacking between the histidine ring and functionalized-SWNT is therefore decreased as compared to the pristine SWNT. However, the above trend does not remain for the binding between the histidine and graphene. The binding of the histidine to the functionalized graphene with -OH and -NH₂ is just slightly weaker than that to the pristine graphene, while its binding to COOH-SWNT becomes a little bit stronger.

Computational chemistry for graphene-based energy applications: progress and challenges

Research in graphene-based energy materials is a rapidly growing area. Many graphene-based energy applications involve interfacial processes. To enable advances in the design of these energy materials, such that their operation, economy, efficiency and durability is at least comparable with fossil-fuel based alternatives, connections between the molecular-scale structure and function of these interfaces are needed. While it is experimentally challenging to resolve this interfacial structure, molecular simulation and computational chemistry can help bridge these gaps. In this Review, we summarise recent progress in the application of computational chemistry to graphene-based materials for fuel cells, batteries, photovoltaics and supercapacitors. We also outline both the bright prospects and emerging challenges these techniques face for application to graphene-based energy materials in future.

Choosing a density functional for modeling adsorptive hydrogen storage: reference quantum mechanical calculations and a comparison of dispersion-corrected density functionals

Various dispersion-corrected density functionals are compared with high level QM data for several model complexes for adsorptive hydrogen storage.

Enthalpy–entropy relations in the acid–base equilibrium of warfarin and 10-hydroxywarfarin; joint experimental and theoretical studies

Warfarin and 10-hydroxywarfarin are structurally similar molecules, however, they exhibit considerably different thermodynamics of acid dissociation. Intramolecular H-bonds and solvent composition are the factors of great importance.

The graphene/nucleic acid nanobiointerface

In this critical review, we present the recent advances in the design and fabrication of graphene/nucleic acid nanobiointerfaces, as well as the fundamental understanding of their interfacial properties and various nanobiotechnological applications.

Intermolecular π/π and H/π interactions in dimers researched by different computational methods

The analysis of π/π and H /π interactions in complexes are a challenging aspect of theoretical research. Due to the different approximations of different levels of theory, results tend to be inconsistent. We compared the reliabilities of HF, SVWN, M06L, PW91, BLYP, B3LYP, BHandHLYP, B97D, MP2, and DFTB-D approaches in researching π/π and H /π interactions by calculating the binding energies of five benzene-containing dimers. The effects of 6-31+G**, 6-311++G** and 6-311++G(2df,2p) basis sets on the results were analyzed too. We found that the DFTB-D and B97D methods combined with the 6-311++G** basis set perform well for dimers that contain π/π and H /π interactions. With high efficiency and satisfactory precision, DFTB-D is helpful for the calculation of complexes containing π/π and H /π stacking. We further calculated the structures and properties of phenylalanine-containing dimers using the DFTB-D and B97D methods. The properties of low energy conformers such as rotational constants, dipole moments and molecular orbitals were also analyzed. These data should be helpful for research into systems that contain π/π and H /π stacking.

Density functional theory based study of molecular interactions, recognition, engineering, and quantum transport in π molecular systems

CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium point are reasonably close to the CCSD(T) results but sometimes slightly deviate from them because interaction energies were not particularly optimized with parameters. Nevertheless, because the electron cloud deforms when neighboring atoms/ions induce an electric field, both vdW-DF2 and PBE0-TS seem to properly reproduce the resulting change of dispersion interaction. Thus, improvements are needed in both vdW-DF2 and PBE0-TS to better describe the interaction energies, while the B97-D3 method could benefit from the incorporation of polarization-driven energy changes that show highly anisotropic behavior. Although the current DFT-D methods need further improvement, DFT-D is very useful for computer-aided molecular design. We have used these newly developed DFT-D methods to calculate the interactions between graphene and DNA nucleobases. Using DFT-D, we describe the design of molecular receptors of π-systems, graphene based electronic devices, metalloporphyrin half-metal based spintronic devices as graphene nanoribbon (GNR) analogs, and graphene based molecular electronic devices for DNA sequencing. DFT-D has also helped us understand quantum phenomena in materials and devices of π-systems including graphene.

Molecular adsorption on graphene

Current studies addressing the engineering of charge carrier concentration and the electronic band gap in epitaxial graphene using molecular adsorbates are reviewed. The focus here is on interactions between the graphene surface and the adsorbed molecules, including small gas molecules (H(2)O, H(2), O(2), CO, NO(2), NO, and NH(3)), aromatic, and non-aromatic molecules (F4-TCNQ, PTCDA, TPA, Na-NH(2), An-CH(3), An-Br, Poly (ethylene imine) (PEI), and diazonium salts), and various biomolecules such as peptides, DNA fragments, and other derivatives. This is followed by a discussion on graphene-based gas sensor concepts. In reviewing the studies of the effects of molecular adsorption on graphene, it is evident that the strong manipulation of graphene's electronic structure, including p- and n-doping, is not only possible with molecular adsorbates, but that this approach appears to be superior compared to these exploiting edge effects, local defects, or strain. However, graphene-based gas sensors, albeit feasible because huge adsorbate-induced variations in the relative conductivity are possible, generally suffer from the lack of chemical selectivity.

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

Computational spectroscopy techniques have become in the last few years an effective means to analyze and assign infrared (IR) spectra of molecular systems of increasing dimensions and in different environments. However, transition from compilation of harmonic data to fully anharmonic simulations of spectra is still underway. The most promising results for large systems have been obtained, in our opinion, by perturbative vibrational approaches based on potential energy surfaces computed by hybrid (especially B3LYP) density functionals and medium size (e.g. SNSD) basis sets. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes and their adsorption on solid supports (organic/inorganic). In this contribution we report the essential results of the first step devoted to isolated monomers and dimers. It is well known that in order to model the vibrational spectra of weakly bound molecular complexes dispersion interactions should be taken into proper account. In this work we have chosen two popular and inexpensive approaches to model dispersion interactions, namely the semi-empirical dispersion correction (D3) and pseudopotential based (DCP) methodologies both in conjunction with the B3LYP functional. These have been used for simulating fully anharmonic IR spectra of nucleobases and their dimers through generalized second order vibrational perturbation theory (GVPT2). We have studied, in particular, isolated adenine, hypoxanthine, uracil, thymine and cytosine, the hydrogen-bonded and stacked adenine and uracil dimers, and the stacked adenine-naphthalene heterodimer. Anharmonic frequencies are compared with standard B3LYP results and experimental findings, while the computed interaction energies and structures of complexes are compared to the best available theoretical estimates.

DNA-protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar

Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteria, including visual inspection. The abundance and structure of the interactions were determined by unequivocally classifying the contacts as either π-π stacking, π-π T-shaped or sugar-π contacts. Three hundred forty-four nucleobase-amino acid π-π contacts (60% of all interactions identified) were identified in 175 of the crystal structures searched. Unprecedented in the literature, 230 DNA-protein sugar-π contacts (40% of all interactions identified) were identified in 137 crystal structures, which involve C-H···π and/or lone-pair···π interactions, contain any amino acid and can be classified according to sugar atoms involved. Both π-π and sugar-π interactions display a range of relative monomer orientations and therefore interaction energies (up to -50 (-70) kJ mol(-1) for neutral (charged) interactions as determined using quantum chemical calculations). In general, DNA-protein π-interactions are more prevalent than perhaps currently accepted and the role of such interactions in many biological processes may yet to be uncovered.

Theoretical study of γ-hexachlorocyclohexane and β-hexachlorocyclohexane isomers interaction with surface groups of activated carbon model

Activated carbon (AC) is employed in drinking water purification without almost any knowledge about the adsorption mechanism of persistent organic pollutants (POPs) onto it. Hexachlorocyclohexane (HCH) is an organochlorinated contaminant present in water and soils of banana crops production zones of the Caribbean. The most relevant isomers of HCH are γ-HCH and β-HCH, both with great environmental persistence. A theoretical study of the influence of AC surface groups (SGs) on HCH adsorption is done in order to help to understand the process and may lead to improve the AC selection process. A simplified AC model consisting of naphthalene with a functional group was used to assess the influence of SGs over the adsorption process. The Multiple Minima Hypersurface (MMH) methodology was employed to study γ-HCH and β-HCH interactions with different AC SGs (hydroxyl and carboxyl) under different hydration and pH conditions. The results obtained showed that association of HCH with SGs preferentially occurs between the axial protons of HCH and SG's oxygen atom, and the most favorable interactions occurring with charged SGs. An increase in carboxylic SGs content is proposed to enhance HCH adsorption onto AC under neutral pH conditions. Finally, this work presents an inexpensive computer aided methodology for preselecting activated carbon SGs content for the removal of a given compound.