Interaction between benzenedithiolate and gold: classical force field for chemical bonding

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.     

Crystal Structure Prediction and Isostructurality of Three Small Molecules

A crystal structure prediction (CSP) study of three small, rigid and structurally related organic compounds (differing only in the position and number of methyl groups) is presented. A tailor‐made force field (TMFF; a non‐transferable force field specific for each molecule) was constructed with the aid of a dispersion‐corrected density functional theory method (the hybrid method). Parameters for all energy terms in each TMFF were fitted to reference data generated by the hybrid method. Each force field was then employed during structure generation. The experimentally observed crystal structures of two of the three molecules were found as the most stable crystal packings in the lists of their force‐field‐optimised structures. A number of the most stable crystal structures were re‐optimised with the hybrid method. One experimental crystal structure was still calculated to be the most stable structure, whereas for another compound the experimental structure became the third most stable structure according to the hybrid method. For the third molecule, the experimentally observed polymorph, which was found to be the fourth most stable form using its TMFF, became the second most stable form. Good geometrical agreements were observed between the experimental structures and those calculated by both methods. The average structural deviation achieved by the TMFFs was almost twice that obtained with the hybrid method. The TMFF approach was extended by exploring the accuracy of a more general TMFF (GTMFF), which involved fitting the force‐field parameters to the reference data for all three molecules simultaneously. This GTMFF was slightly less accurate than the individual TMFFs but still of sufficient accuracy to be used in CSP. A study of the isostructural relationships between these molecules and their crystal lattices revealed a potential polymorph of one of the compounds that has not been observed experimentally and that may be accessible in a thorough polymorph screen, through seeding, or through the use of a suitable tailor‐made additive.     

New energy terms for reduced protein models implemented in an off‐lattice force field

Parameterization and test calculations of a reduced protein model with new energy terms are presented. The new energy terms retain the steric properties and the most significant degrees of freedom of protein side chains in an efficient way using only one to three virtual atoms per amino acid residue. The energy terms are implemented in a force field containing predefined secondary structure elements as constraints, electrostatic interaction terms, and a solvent‐accessible surface area term to include the effect of solvation. In the force field the main‐chain peptide units are modeled as electric dipoles, which have constant directions in α‐helices and β‐sheets and variable conformation‐dependent directions in loops. Protein secondary structures can be readily modeled using these dipole terms. Parameters of the force field were derived using a large set of experimental protein structures and refined by minimizing RMS errors between the experimental structures and structures generated using molecular dynamics simulations. The final average RMS error was 3.7 Å for the main‐chain virtual atoms (C_α atoms) and 4.2 Å for all virtual atoms for a test set of 10 proteins with 58–294 amino acid residues. The force field was further tested with a substantially larger test set of 608 proteins yielding somewhat lower accuracy. The fold recognition capabilities of the force field were also evaluated using a set of 27,814 misfolded decoy structures. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1229–1242, 2001     

Structure‐Independent Conductance of Thiophene‐Based Single‐Stacking Junctions

The experimental investigation of intermolecular charge transport in π‐conjugated materials is challenging. Herein, we describe the investigation of charge transport through intermolecular and intramolecular paths in single‐molecule and single‐stacking thiophene junctions by the mechanically controllable break junction (MCBJ) technique. We found that the ability for intermolecular charge transport through different single‐stacking junctions was approximately independent of the molecular structure, which contrasts with the strong length dependence of conductance in single‐molecule junctions with the same building blocks, and the dominant charge‐transport path of molecules with two anchors transited from an intramolecular to an intermolecular path when the degree of conjugation increased. An increase in conjugation further led to higher binding probability owing to the variation in binding energies, as supported by DFT calculations.     

Peptide Ligands Stabilized by Small Molecules

Bicyclic peptides generated through directed evolution by using phage display offer an attractive ligand format for the development of therapeutics. Being nearly 100‐fold smaller than antibodies, they promise advantages such as access to chemical synthesis, efficient diffusion into tissues, and needle‐free application. However, unlike antibodies, they do not have a folded structure in solution and thus bind less well. We developed bicyclic peptides with hydrophilic chemical structures at their center to promote noncovalent intramolecular interactions, thereby stabilizing the peptide conformation. The sequences of the peptides isolated by phage display from large combinatorial libraries were strongly influenced by the type of small molecule used in the screen, thus suggesting that the peptides fold around the small molecules. X‐ray structure analysis revealed that the small molecules indeed formed hydrogen bonds with the peptides. These noncovalent interactions stabilize the peptide–protein complexes and contribute to the high binding affinity.     

Feeling Inter‐ or Intramolecular Interactions with the Polymer Chain as Probe: Recent Progress in SMFS Studies on Macromolecular Interactions

Single‐molecule force spectroscopy (SMFS) opens new avenues for elucidating the structures and functions of large coiled molecules such as synthetic and biopolymers at the single‐molecule level. In addition, some of the features in the force–extension curves (i.e. force spectra) are closely related to primary/secondary structures of the molecules being stretched. For example, the long force plateau in the DNA stretching curve is related to the double‐helix structure. These features can be regarded as the force fingerprints of individual macromolecules. These force fingerprints can therefore be used as indicators/criteria of single‐molecule manipulation during the measurement of some unknown intra‐ or intermolecular interactions. By comparing the force spectra of a single polymer chain before and after interaction with other molecules, the mode/strength of such molecular interactions can be derived. This Review focuses on recent advances in AFM‐based SMFS studies on molecular interactions in both synthetic and biopolymer systems using a single macromolecular chain as probe, including interactions between nucleic acids and proteins, mechanochemistry of covalent bonds, conformation‐regulated enzymatic reactions, adsorption and desorption of biopolymers on a flat surface or from the nanopore of a carbon nanotube, and polymer interactions in the condensed state.     

DNA base trimers: empirical and quantum chemical ab initio calculations versus experiment in vacuo

A complete scan of the potential‐energy surfaces for selected DNA base trimers has been performed by a molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The resulting most stable/populated structures were then reoptimized at a correlated ab initio level by employing resolution of the identity, Møller–Plesset second‐order perturbation theory (RI‐MP2). A systematic study of these trimers at such a complete level of electronic structure theory is presented for the first time. We show that prior experimental and theoretical interpretations were incorrect in assuming that the most stable structures of the methylated trimers corresponded to planar systems characterized by cyclic intermolecular hydrogen bonding. We found that stacked structures of two bases with the third base in a T‐shape arrangement are the global minima in all of the methylated systems: they are more stable than the cyclic planar structures by about 10 kcal mol^?1. The different behaviors of nonmethylated and methylated trimers is also discussed. The high‐level geometries and interaction energies computed for the trimers serve also as a reference for the testing of recently developed density functional theory (DFT) functionals with respect to their ability to correctly describe the balance between the electrostatic and dispersion contributions that bind these trimers together. The recently reported M052X functional with a polarized triple‐zeta basis set predicts 11 uracil trimer interaction energies with a root‐mean‐square error of 2.3 kcal mol^?1 relative to highly correlated ab initio theoretical calculations.     

Chemically modified fullerene derivatives as photosensitizers in photodynamic therapy: A first‐principles study

The first‐principles density functional theory (DFT) and its time‐dependent approach (TD‐DFT) are used to characterize the electronic structures and optical spectra properties of five chemically modified fullerenes. It is revealed that the metal fullerene derivatives possess not only stronger absorption bands in visible light regions than organically modified fullerene but also the large energy gaps (ΔE_S–T > 0.98 eV) between the singlet ground state and the triplet state, which imply their significant aspect of potential candidates as a photosensitizer. We have found that a new metal‐containing bisfullerene complexes (Pt(C₆₀)₂), with the extended conjugated π‐electrons, much degenerate orbitals and a uniform electrostatic potential surface, behave more pre‐eminent photosensitizing properties than other examined fullerene derivatives. © 2012 Wiley Periodicals, Inc.     

Ab initio Study of Electronic Structure and Properties of Crystalline of 1,5-Diamino-1,2,3,4-tetrazole

Density functional method was applied to study 1,5‐diamino‐1,2,3,4‐tetrazole (DAT, CH₄N₆) in both gaseous and bulk states. The banding and electronic structures of crystalline have been investigated at DFT‐B3LYP/ 6‐311G** level of theory. Relaxed crystal structure compares well with experimental data. The light fluctuation of the frontier orbital, which is mainly formed by atomic orbital of N(4) (heterocycle), is the most reactive part of the molecule, which is in good agreement with the experimental results. The energy gap is 9.035 eV, which indicates that DAT is an insulator. The distribution of electrostatic potential is uniform, indicating DAT is insensitive. The charge density of the intermolecular regions in the plane is not overlaid, indicating that the intermolecular interaction between the neighboring molecules along this direction in the bulk is very weak. The overlap populations of N(1)? N(2) bonds are much less than those of other bonds, therefore the N(1)? N(2) bonds first rupture by external stimuli.     

Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes

Chemical cross-linking of proteins, an established method in protein chemistry, has gained renewed interest in combination with mass spectrometric analysis of the reaction products for elucidating low-resolution three-dimensional protein structures and interacting sequences in protein complexes. The identification of the large number of cross-linking sites from the complex mixtures generated by chemical cross-linking, however, remains a challenging task. This review describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the strategies employing intra- or intermolecular chemical cross-linking and mass spectrometry. The various approaches described in the literature to facilitate detection of cross-linking products and also computer software for data analysis are reviewed. Cross-linking techniques combined with mass spectrometry and bioinformatic methods have the potential to provide the basis for an efficient structural characterization of proteins and protein complexes.     

Extraordinary Changes in the Electronic Structure and Properties of CdS and ZnS by Anionic Substitution: Cosubstitution of P and Cl in Place of S

Unlike cation substitution, anion substitution in inorganic materials such as metal oxides and sulfides would be expected to bring about major changes in the electronic structure and properties. In order to explore this important aspect, we have carried out first‐principles DFT calculations to determine the effects of substitution of P and Cl on the properties of CdS and ZnS in hexagonal and cubic structures and show that a sub‐band of the trivalent phosphorus with strong bonding with the cation appears in the gap just above the valence band, causing a reduction in the gap and enhancement of dielectric properties. Experimentally, it has been possible to substitute P and Cl in hexagonal CdS and ZnS. The doping reduces the band gap significantly as predicted by theory. A similar decrease in the band gap is observed in N and F co‐substituted in cubic ZnS. Such anionic substitution helps to improve hydrogen evolution from CdS semiconductor structures and may give rise to other applications as well.     

A Study of Transition‐Metal Organometallic Complexes Combining 35Cl Solid‐State NMR Spectroscopy and 35Cl NQR Spectroscopy and First‐Principles DFT Calculations

A series of transition‐metal organometallic complexes with commonly occurring metal? chlorine bonding motifs were characterized using ³⁵Cl solid‐state NMR (SSNMR) spectroscopy, ³⁵Cl nuclear quadrupole resonance (NQR) spectroscopy, and first‐principles density functional theory (DFT) calculations of NMR interaction tensors. Static ³⁵Cl ultra‐wideline NMR spectra were acquired in a piecewise manner at standard (9.4 T) and high (21.1 T) magnetic field strengths using the WURST‐QCPMG pulse sequence. The ³⁵Cl electric field gradient (EFG) and chemical shielding (CS) tensor parameters were readily extracted from analytical simulations of the spectra; in particular, the quadrupolar parameters are shown to be very sensitive to structural differences, and can easily differentiate between chlorine atoms in bridging and terminal bonding environments. ³⁵Cl NQR spectra were acquired for many of the complexes, which aided in resolving structurally similar, yet crystallographically distinct and magnetically inequivalent chlorine sites, and with the interpretation and assignment of ³⁵Cl SSNMR spectra. ³⁵Cl EFG tensors obtained from first‐principles DFT calculations are consistently in good agreement with experiment, highlighting the importance of using a combined approach of theoretical and experimental methods for structural characterization. Finally, a preliminary example of a ³⁵Cl SSNMR spectrum of a transition‐metal species (TiCl₄) diluted and supported on non‐porous silica is presented. The combination of ³⁵Cl SSNMR and ³⁵Cl NQR spectroscopy and DFT calculations is shown to be a promising and simple methodology for the characterization of all manner of chlorine‐containing transition‐metal complexes, in pure, impure bulk and supported forms.     

Density functional theory study of calix[4]arene‐N‐azacrown‐5, calix[4]arene‐N‐phenyl‐azacrown‐5, and their complexes with alkali‐metal cations: Na+, K+, and Rb+

Theoretical studies of 1,3‐alternate‐25,27‐bis(1‐methoxyethyl)calix[4]arene‐azacrown‐5 ( L₁ ), 1,3‐alternate‐25,27‐bis(1‐methoxyethyl)calix[4]arene‐N‐phenyl‐azacrown‐5 ( L₂ ), and the corresponding complexes M⁺/ L of L₁ and L₂ with the alkali‐metal cations: Na⁺, K⁺, and Rb⁺ have been performed using density functional theory (DFT) at B3LYP/6‐31G* level. The optimized geometric structures obtained from DFT calculations are used to perform natural bond orbital (NBO) analysis. The two main types of driving force metal–ligand and cation–π interactions are investigated. The results indicate that intermolecular electrostatic interactions are dominant and the electron‐donating oxygen offer lone pair electrons to the contacting RY* (1‐center Rydberg) or LP* (1‐center valence antibond lone pair) orbitals of M⁺ (Na⁺, K⁺, and Rb⁺). What's more, the cation–π interactions between the metal ion and π‐orbitals of the two rotated benzene rings play a minor role. For all the structures, the most pronounced changes in geometric parameters upon interaction are observed in the calix[4]arene molecule. In addition, an extra pendant phenyl group attached to nitrogen can promote metal complexation by 3D encapsulation greatly. In addition, the enthalpies of complexation reaction and hydrated cation exchange reaction had been studied by the calculated thermodynamic data. The calculated results of hydrated cation exchange reaction are in a good agreement with the experimental data for the complexes. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Electrostatic Energies in the 1,4‐Dichlorobenzene Polymorph Crystals: the Role of Charge Density Overlap Effects in Crystal Packing Analysis

Electrostatic and polarization energies for the three known polymorphic crystal structures of 1,4‐dichlorobenzene, as well as for one particularly stable virtual crystal structure generated by computer search, were calculated by a new accurate numerical integration method over static molecular charge densities obtained from high level ab initio molecular‐orbital calculations. Results are compared with those from standard empirical atom‐atom force fields. The new electrostatic energies, which include charge density overlap (penetration) effects, are seen to be much larger than and sometimes of opposite sign to those derived from point‐charge models. None of the four polymorphs is substantially more stable than the others on electrostatic‐energy grounds. Molecule‐molecule electrostatic energies have been calculated for the more important molecular pairs in each of the four structures; trends are found to be very different from those indicated by point‐charge energies or by total energies estimated with a parametric atom‐atom force field. Conclusions based exclusively on analysis of intermolecular atom contacts and point‐charge electrostatics may need to be modified in the light of the new kind of calculation.     

Effect of water on zinc (II), cadmium (II) complexes with pyridylimidazole: Theoretical study of stability and electronic spectrum

The geometry structures of complexes such as [Zn(PIm)₂(H₂O)] and [Cd(PIm)₂(H₂O)₂] [PIm = (2‐(2′‐pyridyl) imidazole)] are optimized by density functional theory (DFT) B3LYP methods. On the basis of their stable structures, the stability of the coordinated water existing in the complexes is analyzed quantitatively in terms of the interaction between the central metal and the coordinated water. The interaction energy of the Zn pyridylimidazole complex increased obviously by considering the intermolecular hydrogen bond (O? H…N). The theoretical calculation well explained penta‐ and hexa‐coordinated conformation, respectively, in Zn and Cd pyridylimidazole complexes. The spectral properties of the Zn Cd complexes have been studied by time‐dependent density functional theory (TD‐DFT). The calculation results show that the coordinated waters in Cd complexes have little effect on their spectral properties. While the axially coordinated waters in Zn pyridylimidazole cause a red shift in the absorption wavelength and change the pattern of charge transfer as a result of the effect of polarization from intermolecular hydrogen bond. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Crystallization Force—A Density Functional Theory Concept for Revealing Intermolecular Interactions and Molecular Packing in Organic Crystals

Organic molecules are prone to polymorphic formation in the solid state due to the rich diversity of functional groups that results in comparable intermolecular interactions, which can be greatly affected by the selection of solvent and other crystallization conditions. Intermolecular interactions are typically weak forces, such as van der Waals and stronger short‐range ones including hydrogen bonding, that are believed to determine the packing of organic molecules during the crystal‐growth process. A different packing of the same molecules leads to the formation of a new crystal structure. To disclose the underlying causes that drive the molecule to have various packing motifs in the solid state, an electronic concept or function within the framework of conceptual density functional theory has been developed, namely, crystallization force. The concept aims to describe the local change in electronic structure as a result of the self‐assembly process of crystallization and may likely quantify the locality of intermolecular interactions that directs the molecular packing in a crystal. To assess the applicability of the concept, 5‐methyl‐2‐[(2‐nitrophenyl)amino]‐3‐thiophenecarbonitrile, so‐called ROY, which is known to have the largest number of solved polymorphs, has been examined. Electronic calculations were conducted on the seven available crystal structures as well as on the single molecule. The electronic structures were analyzed and crystallization force values were obtained. The results indicate that the crystallization forces are able to reveal intermolecular interactions in the crystals, in particular, the close contacts that are formed between molecules. Strong correlations exist between the total crystallization force and lattice energy of a crystal structure, further suggesting the underlying connection between the crystallization force and molecular packing.     

Tailor-made force fields for crystal-structure prediction

A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.     

Adsorption induced surface-stress sensing signal originating from both vertical interface effects and intermolecular lateral interactions

This research investigates the origin of specific molecule-adsorption induced surface-stress for micro/nano-cantilever bio/chemical sensors. Systematic discussion is presented on the contribution from types of molecule interactions to the generated surface-stress sensing signal. With the main arguments verified by our micro-cantilever sensing experiments, the origin of the adsorption induced surface-stress is, for the first time, clearly categorized into interface vertical effects and lateral interactions, which helps to comprehensively understand the surface-stress generation and overall to optimize the sensing performance of micro-cantilever chemo-mechanical sensors. The key findings of this research are that, vertically at the molecule adsorption surface, interfacial energy change and charge redistribution are the main origins of the generated surface-stress. More importantly, intermolecular lateral interactions may make a more significant contribution to the nano-mechanical surface-stress response. Compared with other lateral interactions like van der Waals force and the electrostatic coulombic effect, intermolecular hydrogen-bond intensity and steric factor easily cause much greater disparity in surface-stress.