Anticooperative Effects Research Articles

Study of Two-Photon induced excited state absorption of Three-Branched triphenylamine Derivatives: Cooperative and Anti-Cooperative effect of electron transition in the excited state

For multi-branched molecules, intramolecular cooperative effect can significantly enhance the molecular nonlinear optical absorption. Three triphenylamine-cored compounds (N1, N2 and N3) with three branches are synthesized to study the cooperative and anti-cooperative effect of electron transition in the excited state on two-photon absorption (TPA) and excited state absorption (ESA). Molecular polarization of these multi-branched triphenylamine derivatives is regulated by changing the molecular symmetry and the planarity of peripheral branches, to regulate their charge distribution and electron transition characteristics in the excited state. Here, we show that due to electronic coupling and interaction between certain branches, the asymmetric distribution of electron clouds in the excited states of these multi-branched molecules will lead to an enhancement of their TPA and ESA cross-sections, which is known as the cooperative effect of electron transitions. On the contrary, electronic coupling and interaction among all branches will lead to a highly symmetric distribution of electron clouds in the excited states of these multi-branched molecules, which will cause anti-cooperative effects and result in significant attenuation of TPA and ESA cross-sections.

A many-body energy decomposition analysis (MB-EDA) scheme based on a target state optimization self-consistent field (TSO-SCF) method.

In this paper, we combine an energy decomposition analysis (EDA) scheme with many-body expansion (MBE) to develop a MB-EDA method to study the cooperative and anti-cooperative effects in molecular cluster systems. Based on the target state optimization self-consistent field (TSO-SCF) method, the intermolecular interaction energy can be decomposed into five chemically meaningful terms, i.e., electrostatic, exchange, polarization, charge transfer and dispersion interaction energies. MB-EDA can decompose each of these terms in MBE. This MB-EDA has been applied to 3 different cluster systems: water clusters, ionic liquid clusters, and acetonitrile-methane clusters. This reveals that electrostatic, exchange, and dispersion interactions are highly pairwise additive in all systems. In water and ionic liquid clusters, the many-body effects are significant in both polarization and charge transfer interactions, but are cooperative and anti-cooperative, respectively. For acetonitrile-methane clusters, which do not involve hydrogen bonds or charge-charge Coulombic interactions, the many-body effects are quite small. The chemical origins of different many-body effects are deeply analyzed. The MB-EDA method has been implemented in Qbics (https://qbics.info) and can be a useful tool for understanding the many-body behavior in molecular aggregates at the quantum chemical level of theory.

Anticooperative Supramolecular Oligomerization Mediated by V-Shaped Monomer Design and Unconventional Hydrogen Bonds.

After more than three decades of extensive investigations on supramolecular polymers, strategies for self-limiting growth still remain challenging. Herein, we exploit a new V-shaped monomer design to achieve anticooperatively formed oligomers with superior robustness and high luminescence. In toluene, the monomer-oligomer equilibrium is shifted to the monomer side, enabling the elucidation of the molecular packing modes and the resulting (weak) anticooperativity. Steric effects associated with an antiparallel staircase organization of the dyes are proposed to outcompete aromatic and unconventional B-F⋅⋅⋅H-N/C interactions, restricting the growth at the stage of oligomers. In methylcyclohexane (MCH), the packing modes and the anticooperativity are preserved; however, pronounced solvophobic and chain-enwrapping effects lead to thermally ultrastable oligomers. Our results shed light on understanding anticooperative effects and restricted growth in self-assembly.

Anticooperative Supramolecular Oligomerization Mediated by V‐Shaped Monomer Design and Unconventional Hydrogen Bonds

AbstractAfter more than three decades of extensive investigations on supramolecular polymers, strategies for self‐limiting growth still remain challenging. Herein, we exploit a new V‐shaped monomer design to achieve anticooperatively formed oligomers with superior robustness and high luminescence. In toluene, the monomer‐oligomer equilibrium is shifted to the monomer side, enabling the elucidation of the molecular packing modes and the resulting (weak) anticooperativity. Steric effects associated with an antiparallel staircase organization of the dyes are proposed to outcompete aromatic and unconventional B−F⋅⋅⋅H−N/C interactions, restricting the growth at the stage of oligomers. In methylcyclohexane (MCH), the packing modes and the anticooperativity are preserved; however, pronounced solvophobic and chain‐enwrapping effects lead to thermally ultrastable oligomers. Our results shed light on understanding anticooperative effects and restricted growth in self‐assembly.

Do weak interactions affect the biological behavior of DNA? A DFT study of CpG island-like chains.

The origin, stability, and contribution to the formation of noncovalent interactions, such as hydrogen bonds and π - π stacking, have been already widely discussed. However, there are few discussions about the relevance of these weak interactions in DNA performance. In this work, we seek to shed light on the effect of hydrogen bonds and π - π stacking interactions on the biological behavior of DNA through the description of these intermolecular forces in CpG island-like (GC-rich) chains. Furthermore, we made some comparisons with TATA box-like (TA-rich) chains in order to describe hydrogen bond and π - π stacking interactions as a function of the DNA sequence. For hydrogen bonds, we found that there is not a significant effect related to the number of base pairs. Whereas for π - π stacking interactions, the energy tended to decrease as the number of base pairs increased. We observed anticooperative effects for both hydrogen bonds and π - π stacking interactions. These results are in contrast with those of TATA box-like chains since cooperative and additive effects were found for both hydrogen bonds and π - π stacking, respectively. Based on the chemical hardness and density of states, we can conclude that proteins may interact easier with GC-rich chains. We conclude that regardless of the chain length, a protein could interact more easily with these genomics regions because the π - π stacking energies did not increase as a function of the number of base pairs, making, for the first time, a first approximation of the influence of noncovalent interaction on DNA behavior. We did all this work by means of DFT framework included in the DMol3 code (M06-L/DNP). Graphical Abstract Cartoon representation of how nocovalent interactions affect the interaction of DNA with a protein, i.e., how hydrogen bond and π - π stacking interactions influence the biological behavior of DNA.

Pseudo-Bifurcated Chalcogen Bond in Crystal Engineering

The concept of pseudo-bifurcated chalcogen bond has been proposed for the first time in this paper. It was found that the anticooperative effects between two chalcogen bonds of the pseudo-bifurcated chalcogen bond are not very large as compared to those of the true bifurcated noncovalent bond. According to the nature of pseudo-bifurcated chalcogen bond, we designed some strong pseudo-bifurcated chalcogen bond synthons. The binding energy of the strongest pseudo-bifurcated chalcogen bond attains about 27 kcal/mol. These strong pseudo-bifurcated chalcogen bond synthons have great potential as building blocks in crystal engineering.

Ion-pair recognition based on halogen bonding: a case of the crown-ether receptor with iodo-trizole moiety

The development of halogen-bond-based ditopic receptors capable of binding simultaneously both a cation and an anion has attracted recent research interest. In this work, the crown-ether receptor 1, which consists of an iodo-trizole moiety for anion recognition through halogen bonding and a Lewis-basic center for cation binding, was investigated using density functional theory calculations. The structural and energetic features for the complexes of 1 with single cations, single halide anions, and ion pairs were explored. Intermolecular interactions in these complexes were systematically analyzed by the atoms in molecules and noncovalent interaction index methods. The presence of the coordinated cation significantly increases the anion-binding affinity, while the binding of halide anions has a slight influence on the cation-binding affinity. Anti-cooperative effects were found in the ion-pair recognition of 1, due to the strong attraction between the two counterions in the complexes. The solvent weakens the interaction strength considerably, and anti-cooperativity becomes very small in solvent. The results reported in this work are of fundamental importance in the design of ion-pair receptors based on halogen bonding.

Linear σ‐Hole Bonding Dimers and Trimers Between Dihalogen Molecules XY (X, Y=Cl, Br) and Carbon Monoxide

AbstractIntermolecular interactions between CO and dihalogen molecules XY (X, Y=Cl, Br) were investigated at MP2/aug‐cc‐pVDZ level without and with counterpoise method, and single point calculations at CCSD(T)/aug‐cc‐pVDZ level were performed. XY can interact with one or two CO to form linear σ‐hole bonding dimer or trimer. Their optimized geometries, stretching modes and interaction energies were investigated. The X⋅⋅⋅C (or Y⋅⋅⋅C) interaction is stronger and more competitive than X⋅⋅⋅O (or Y⋅⋅⋅O) interaction, so the OC⋅⋅⋅X−Y⋅⋅⋅CO complex is stronger and more competitive than the CO⋅⋅⋅X−Y⋅⋅⋅OC complex. The interaction strengths of trimeric complexes are dependent upon the property of XY, andthe anticooperative or diminutive effects were observed for them. Electrostatic interaction is the dominant net driving force for the formation of these dimers based on EDA analysis. The formation of two linear halogen bonds in each trimer was identified by bond paths and green circle isosurfaces appearing between the halogen and C (or O) atoms. The results would provide valuable insight into the competition and cooperativity of linear halogen bonds.

Cooperative and anticooperative effects in resonance assisted hydrogen bonds in merged structures of malondialdehyde.

We analyzed non-additive effects in resonance assisted hydrogen bonds (RAHBs) in different β-enolones, which are archetypal compounds of these types of interactions. For this purpose, we used (i) potential energy curves to compute the formation energy, ΔE, of the RAHBs of interest in different circumstances along with (ii) tools offered by quantum chemical topology, namely, the Quantum Theory of Atoms In Molecules (QTAIM) and the Interacting Quantum Atoms (IQA) electronic energy partition. We established the effect that a given H-bond exerts over ΔE associated with another RAHB, determining in this way the cooperativity or the anticooperativity of these interactions. The mesomeric structures and the QTAIM delocalisation indices are consistent with the determined cooperative or anticooperative character of two given RAHBs. The HB cooperativity and anticooperativity studied herein are directly reflected in the IQA interaction energy E, but they are modulated by the surrounding hydrocarbon chain. The IQA decomposition of ΔEcoop, a measure of the cooperativity between a pair of interacting RAHBs, indicates that the analyzed H-bond cooperative/anticooperative effects are associated with greater/smaller (i) strengthening of the pseudo-bicyclic structure of the compounds of interest and (ii) electron localisations with its corresponding changes in the intra and intermolecular exchange-correlation contributions to ΔE. Overall, we expect that this investigation will provide valuable insights into the interplay among hydrogen bonded atoms and the π system in RAHBs contributing in this way to the understanding of the general features of H-bonds.

Evolution of the hydrogen-bonding motif in the melamine-cyanuric acid co-crystal: a topological study.

The melamine (M)/cyanuric acid (CA) supramolecular system is perhaps one of the most exploited in the field of self-assembly because of the high complementarity of the components. However, it is necessary to investigate further the factors involved in the assembly process. In this study, we analyzed a set of 13 M n /CA m clusters (with n , m=1, 2, 3), taken from crystallographic data, to characterize the nature of the hydrogen bonds involved in the self-assembly of these components as well as to provide greater understanding of the phenomenon. The calculations were performed at the B3LYP/6-311++G(d,p) and ω-B97XD (single point) levels of theory, and the interactions were analyzed within the framework of the quantum theory of atoms in molecules and by means of molecular electrostatic potential maps. Our results show that the stablest structure is the rosette-type motif and the aggregation mechanism is governed by a combination of cooperative and anticooperative effects. Our topological results explain the polymorphism in the self-assembly of coadsorbed monolayers of M and CA. Graphical abstract The aggregation steps of the melamine-cyanuric co-crystal is driven by a hydrogen-bonded network which is governed by a complex combination of cooperative and anticooperative effects.

Fluorines in tetrafluoromethane as halogen bond donors: Revisiting address the nature of the fluorine'sσhole

It has been demonstrated in several instances that the 0.001 a.u. (electrons per bohr3) isodensity mapped electrostatic surface potentials on the fluorines along the outermost extensions of the CF covalent bonds in tetrafluoromethane (CF4) are entirely negative, they are thereby unable to engage in σhole bonding interactions with the negative sites on another molecules. In this study, we have attempted at resolving this controversy by performing various high-level electronic structure calculations with Quadratic Configuration Integrals of Singles and Doubles QCISD(full), second-order Møller–Plesset MP2(full), and 12 other Density Functional Theory (DFT) based functionals with and without dispersion corrections, all in conjunction with the 6–311++G(2d,2p) basis set. The results achieved with all the levels of theory utilized suggest that the fluorine's σholes in CF4 are positive regardless of the 0.001-, 0.0015-, and 0.002-a.u. isodensity mapped electrostatic surfaces examined. Because of this specific quality, the fluorines in CF4 have displayed their capacities to form not only 1:1 clusters with the Lewis bases such as water (H2O), ammonia (NH3), formaldehyde (H2CO), hydrogen fluoride (HF), and hydrogen cyanide (HCN), but also 1:2, 1:3, and 1:4 clusters with the latter three randomly chosen Lewis bases. Various topological and nontopological features obtained from applications of atoms in molecules, noncovalent interaction reduced-density-gradient and natural bond orbital analytical tools reveal that the N···F, O···F, and F···F long-ranged interactions developed between the interacting monomers in H3N···FCF3, H2O···FCF3, and (YD)n=1–4···F4C (YD = H2CO, HCN, and HF) are reminiscent of halogen bonding. The nonadditive cooperative and anticooperative energetic effects emerged on cluster formations are discussed in detail. © 2015 Wiley Periodicals, Inc.

How Strong Is Hydrogen Bonding in Ionic Liquids? Combined X-ray Crystallographic, Infrared/Raman Spectroscopic, and Density Functional Theory Study

Hydrogen bonding in ionic liquids based on the 1-(2'-hydroxylethyl)-3-methylimidazolium cation ([C₂OHmim](+)) and various anions ([A](-)) of differing H-bond acceptor strength, viz. hexafluorophosphate [PF6](-), tetrafluoroborate [BF₄](-), bis(trifluoromethanesulfonimide) [Tf₂N](-), trifluoromethylsulfonate [OTf](-), and trifluoroacetate [TFA](-), was studied by a range of spectroscopic and computational techniques and, in the case of [C₂OHmim][PF6], by single crystal X-ray diffraction. The first quantitative estimates of the energy (E(HB)) and the enthalpy (-ΔH(HB)) of H-bonds in bulk ILs were obtained from a theoretical analysis of the solid-state electron-density map of crystalline [C₂OHmim][PF6] and an analysis of the IR spectra in crystal and liquid samples. E(HB) for OH···[PF6](-) H-bonds amounts to ~3.4-3.8 kcal·mol(-1), whereas weaker H-bonds (2.8-3.1 kcal·mol(-1)) are formed between aromatic C2H group of imidazolium ring and the [PF6](-) anion. The enthalpy of the OH···[A](-) H-bonds follows the order: [PF6] (2.4 kcal·mol(-1)) < [BF₄] (3.3 kcal·mol(-1)) < [Tf₂N] (3.4 kcal·mol(-1)) < [OTf] (4.7 kcal·mol(-1)l) < [TFA] (6.2 kcal·mol(-1)). The formation of aggregates of self-associated [C₂OHmim](+) cations is present in liquid [C₂OHmim][PF6], [C₂OHmim][BF₄], and [C₂OHmim][Tf₂N], with the energy of the OH···OH H-bonds amounting to ~6 kcal·mol(-1). Multiple secondary interactions in the bulk ILs influence their structure, vibrational spectra, and H-bond strength. In particular, these interactions can blue-shift the stretching frequencies of the CH groups of the imidazolium ring in spite of red-shifting CH···[A](-) H-bonds. They also weaken the H-bonding in the IL relative to the isolated ion pairs, with these anticooperative effects amounting to ca. 50% of the E(HB) value.

Generation of a Dynamic System of Three‐Dimensional Tetrahedral Polycatenanes

Generation of a Dynamic System of Three‐Dimensional Tetrahedral Polycatenanes

Cooperativity between hydrogen bonds and beryllium bonds in (H2O)nBeX2 (n = 1–3, X = H, F) complexes. A new perspective

The interaction of BeX(2) (X = H, F) with water molecules has been analyzed at the B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) level of theory. The formation of strong beryllium bonds between water molecules and the BeX(2) derivative triggers significant electron density redistribution within the whole system, resulting in significant changes in the proton donor and proton acceptor capacity of the water molecules involved. Hence, significant cooperative and anti-cooperative effects are present, explaining why there is no case in which the global minimum corresponds to a tetracoordinated beryllium atom. In fact, the most stable clusters can be viewed as the result of the attachment of BeX(2) to the water trimer and the water dimer, respectively, and not as the result of the solvation of the BeX(2) molecule. We have also shown that the decomposition of the interaction energy into atomic components is a reliable quantitative tool to describe all the closed-shell interactions present in the clusters investigated herein, namely hydrogen bonds, beryllium bonds and dihydrogen bonds. Indeed, we have shown that the changes in the atomic energy components are correlated with the changes in the strength of these interactions, and they provide a quantitative measure of cooperative effects directly in terms of energies.

A theoretical study of cooperative and anticooperative effects on hydrogen-bonded clusters of water and the cyanuric acid

Ab initio and density functional calculations are used to analyse the interaction between a molecule of the cyanuric acid and one, two and three molecules of water at B3LYP/6-311++ G(d,p) and MP2/6-311++ G(d,p) computational levels. Also, the cooperative effect (CE) in terms of the stabilisation energy of clusters is calculated and discussed. Depending on the geometry of clusters under study, the cooperative, non- or anti-CE was found with an increasing cluster size. Red shifts of N–H and C = O stretching frequencies illustrate a good dependence on the CE. The atoms in molecules theory is used to analyse the CE on topological parameters.

Evidence that Interaction between Conserved Residues in Transmembrane Helices 2, 3, and 7 Are Crucial for Human VPAC1 Receptor Activation

The VPAC(1) receptor belongs to family B of G protein-coupled receptors (GPCR-B) and is activated upon binding of the vasoactive intestinal peptide (VIP). Despite the recent determination of the structure of the N terminus of several members of this receptor family, little is known about the structure of the transmembrane (TM) region and about the molecular mechanisms leading to activation. In the present study, we designed a new structural model of the TM domain and combined it with experimental mutagenesis experiments to investigate the interaction network that governs ligand binding and receptor activation. Our results suggest that this network involves the cluster of residues Arg(188) in TM2, Gln(380) in TM7, and Asn(229) in TM3. This cluster is expected to be altered upon VIP binding, because Arg(188) has been shown previously to interact with Asp(3) of VIP. Several point mutations at positions 188, 229, and 380 were experimentally characterized and were shown to severely affect VIP binding and/or VIP-mediated cAMP production. Double mutants built from reciprocal residue exchanges exhibit strong cooperative or anticooperative effects, thereby indicating the spatial proximity of residues Arg(188), Gln(380), and Asn(229). Because these residues are highly conserved in the GPCR-B family, they can moreover be expected to have a general role in mediating function.

Hydrophobic interactions in model enclosures from small to large length scales: non-additivity in explicit and implicit solvent models.

The binding affinities between a united-atom methane and various model hydrophobic enclosures were studied through high accuracy free energy perturbation methods (FEP). We investigated the non-additivity of the hydrophobic interaction in these systems, measured by the deviation of its binding affinity from that predicted by the pairwise additivity approximation. While only small non-additivity effects were previously reported in the interactions in methane trimers, we found large cooperative effects (as large as -1.14 kcal mol(-1) or approximately a 25% increase in the binding affinity) and anti-cooperative effects (as large as 0.45 kcal mol(-1)) for these model enclosed systems. Decomposition of the total potential of mean force (PMF) into increasing orders of multi-body interactions indicates that the contributions of the higher order multi-body interactions can be either positive or negative in different systems, and increasing the order of multi-body interactions considered did not necessarily improve the accuracy. A general correlation between the sign of the non-additivity effect and the curvature of the solute molecular surface was observed. We found that implicit solvent models based on the molecular surface area (MSA) performed much better, not only in predicting binding affinities, but also in predicting the non-additivity effects, compared with models based on the solvent accessible surface area (SASA), suggesting that MSA is a better descriptor of the curvature of the solutes. We also show how the non-additivity contribution changes as the hydrophobicity of the plate is decreased from the dewetting regime to the wetting regime.

Coarse-grained lattice model for investigating the role of cooperativity in molecular recognition

Equilibrium aspects of the molecular recognition of rigid biomolecules are investigated using coarse-grained lattice models. The analysis is carried out in two stages. First, an ensemble of probe molecules is designed with respect to the target biomolecule. The recognition ability of the probe ensemble is then investigated by calculating the free energy of association. The influence of cooperative and anticooperative effects accompanying the association of the target and probe molecules is studied. Numerical findings are presented and compared to analytical results which can be obtained in the limit of dominating cooperativity and in the mean-field formulation of the models.

Theoretical study of properties of H bonds and intermolecular interactions in linear cis-,trans-cyclotriazane clusters (n=2–8)

Our calculations based upon Becke's three-parameter functional of density-functional theory (DFT) with the correlation of Lee, Yang, and Parr (B3LYP), natural bond orbital, and atoms in molecule indicate that in drastic contrast to most H-bonded systems, the anticooperative and cooperative effects coexist in the linear H-bonded cis-,trans (c,t)-cyclotriazane clusters (n = 2-8). As cluster size increases, the properties along the H-bonded chains at trans-positions take on the unexpectedly anticooperative changes which are reflected in elongation of the N...H hydrogen bonds, frequency blueshift in the N-H stretching vibrations, decay in the n(N)-->sigma*(N-H) charge transfers, and weakening of strengths of the N...H bonds. And the cooperative changes in the corresponding properties for the cis- H-bonded chains are observed to be concurrent with the anticooperativities. The rise and fall in the n(N)-->sigma*(N-H) interactions cause increment and decrement in capacities of the clusters to concentrate electrons at the bond critical points of the N...H bonds, and thereby leading to the cooperative and the anticooperative changes especially in the N...H lengths and the N-H stretching frequencies. In terms of three-body symmetry-adapted perturbation theory (three-body SAPT), the first exchange nonadditivity plays a more important role in stabilizing trimer than the nonadditive induction. However, the dominance of the first exchange nonadditivity in three-body interaction unexpectedly triggers the anticooperative effect that counteracts the concurrent cooperative effect. According to the SAPT(DFT), which is a combination of SAPT with asymptotically corrected DFT, DFT/B3LYP is able to succeed in describing the electrostatic, exchange, and induction components, but fails to yield satisfactory interaction energies due to the fact that about 40% of short-range dispersion energy is neglected by the DFT, which is different from many H-bonded described well by the DFT. A quantum cluster equilibrium model illustrates that the c,t-cyclotriazane liquid phase exhibits a weak cooperative effect.

A many-body model to study proteins. II. Incidence of many-body polarization effects on the interaction of the calmodulin protein with four Ca2+ dications and with a target enzyme peptide

The origin of the interactions occurring in the calmodulin protein interacting with one of its target peptide and counterions, and binding four calcium dications, has been investigated in the gas phase, using the many-body model presented in Paper I [Masella and Cuniasse, J. Chem. Phys. 119, 1866 (2003)] and a classical pairwise force field. As compared to the latter force field, the many-body model is shown to provide a geometrical description of the calmodulin/target peptide structure in better agreement with the x-ray experimental one, and a better description of the Ca2+ binding sites (as compared to “small molecule” structures reported in the Cambridge Structural Database). Regarding the energy, both models provide qualitatively a similar description of the interactions occurring in the calmodulin/target peptide system. However, quantitatively, the pairwise model predicts interaction energies greater by about 25% as compared to the many-body one in the case of calmodulin/Ca2+ interactions. This is due to the inability of pairwise force fields to account for the strong anticooperative effects predicted to occur in [Ca,(carboxylate)n]2−n systems by both the many-body model and quantum computations. Hence, the new many-body model appears to be well suited for describing proteinic systems interacting with cations, both in terms of geometry and energy.