Parameterization of a B3LYP specific correction for non-covalent interactions and basis set superposition error on a gigantic dataset of CCSD(T) quality non-covalent interaction energies

A vast number of non-covalent interaction energies at the counterpoise corrected CCSD(T) level have been collected from the literature to build a diverse new dataset. The whole dataset, which consists of 2027 CCSD(T) energies, includes most of the published data at this level. A large subset of the data was then used to train a novel, B3LYP specific, empirical correction scheme for non-covalent interactions and basis set superposition error (abbreviated as B3LYP-MM). Results obtained with our new correction scheme were directly compared to benchmark results obtained with B3LYP-D3(1) and M06-2X(2) (two popular density functions designed specifically to accurately model non-covalent interactions). For non-covalent complexes dominated by dispersion or dipole-dipole interactions all three tested methods give accurate results with the medium size aug-cc-pVDZ(3-6) basis set with MUE's of 0.27 (B3LYP-MM), 0.32 (B3LYP-D3) and 0.47 kcal/mol (M06-2X) (with explicit counterpoise corrections). These results validate both B3LYP-D3 and M06-2X for interactions of this type using a much larger data set than was presented in prior work. However, our new dispersion correction scheme shows some clear advantages for dispersion and dipole-dipole dominated complexes with the small LACVP* basis set, which is very popular in use due to its low associated computational cost: The MUE for B3LYP-MM with the LACVP* basis set for this subset of complexes (without explicit counterpoise corrections) is only 0.28 kcal/mol, compared to 0.65 kcal/mol for M06-2X or 1.16 kcal/mol for B3LYP-D3. Additionally, our new correction scheme also shows major improvements in accuracy for hydrogen-bonded systems and for systems involving ionic interactions, for example cation-π interactions. Compared to B3LYP-D3 and M06-2X, we also find that our new B3LYP-MM correction scheme gives results of higher or equal accuracy for a large dataset of conformer energies of di- and tripeptides, sugars, and cysteine.     

Molecular self-assemblies of a pi-conjugated redox-active bipyridinium cation with magnetic dimetallic oxalate-bridged trimeric clusters

A series of molecular assemblies constructed from a pi-conjugated redox-active bipyridinium cation, 1,4-bis(4'-pyridyl-1'-pyridinio)phthalazine (Bpyph), and magnetic dimetallic oxalate-bridged trimeric clusters, has been synthesized and characterized by elemental analysis, IR, TGA, X-ray single-crystal diffraction and magnetic susceptibility studies. The molecular assemblies formulated as (Bpyph)2{M(II)(H2O)2[M(III)(C2O4)3]2}.12.5H2O [for M(III) = Fe; M(II) = Mn (1) or Co (2); for M(III) = Cr; M(II) = Mn (3) or Co4] are isostructural, their structures feature an alternative arrangement of Bpyph2+ cations and the linear trimeric oxalate complexes {M(II)(H2O)2[M(III)(C2O4)3]2} along all three crystallographic axes, in which the dimetallic trimers form two distinct homo-chiral helices along the b axis via intermolecular hydrogen bonding interactions. Within each trimeric cluster, the two M(III) sites have opposite chirality (Delta and Lambda). Studies on the magnetic properties reveal the presence of antiferromagnetic exchange interactions within the trimeric clusters for the Fe2M and ferromagnetic for the Cr2M series.     

Ternary Rhodium Borides A3Rh5B2 (A = Mg,Sc) and Quaternary Derivatives A2MRh5B2. Preparation,Crystal Structure (M = Main Group and 3 d Elements), and Magnetism (M = Mn,Fe)

The new ternary rhodium borides Mg₃Rh₅B₂ and Sc₃Rh₅B₂ (P4/mbm, Z = 2; a = 943.4(1) pm, c = 292.2(1) pm and a = 943.2(1) pm, c = 308.7(1) pm, respectively) crystallize with the Ti₃Co₅B₂ type structure. Mg and Sc may in part be substituted by a variety of elements M. For M = Si and Fe, homogeneity ranges were found according to A_3–xM_xRh₅B₂ with 0 ≤ x ≤ 1.0 for A = Sc and with x up to 1.5 for A = Mg. Quaternary compounds with x = 1 (A₂MRh₅B₂: A/M in short) were prepared with M = Be, Al, Si, P, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ga, Ge, As, Sn (Co, Ni only with A = Mg; Sn only with A = Sc; P, As with deficiencies). Single crystal X‐ray investigations show an ordered substitutional variant of the Ti₃Co₅B₂ type in which the M atoms are arranged in chains along [001] with intrachain and interchain M–M distances of about 300 pm and 660 pm, respectively. Measuring the magnetisation (1.7 K–800 K) of the phases Mg/Mn, Sc/Mn, Mg/Fe, and Sc/Fe reveals antiferromagnetic interactions in the first and dominating ferromagnetic intrachain interactions in the remaining ones. Interchain interactions of antiferromagnetic nature are evident in Sc/Mn and Mg/Fe leading to metamagnetism below T_N = 130 K, while Sc/Fe behaves ferromagnetically below T_C = 450 K. The overall trend towards stronger ferromagnetic interactions with increasing valence electron concentration is obvious.     

Metastable Chiral Azobenzenes Stabilized in a Double Racemate

The self‐assembly of chiral organic chromophores is gaining huge significance due to the abundance of supramolecular chirality found in natural systems. We report an interdigitated molecular assembly involving axially chiral octabrominated perylenediimide (OBPDI) which transfers chiral information to achiral aromatic moieties. The crystalline two‐component assemblies of OBPDI and electron‐rich aromatic units were facilitated through π‐hole???π donor–acceptor interactions, and the charge‐transfer characteristics in the ground and excited states of the OBPDI cocrystals were established through spectroscopic and theoretical techniques. The OBPDI cocrystals entail a remarkable homochiral segregation of P and M enantiomers of both molecular entities in the same crystal system, leading to twisted double‐racemic arrangements. Synergistically engendered cavities with the stored chiral information of the twisted OBPDI stabilize higher‐energy P/M enantiomers of trans‐azobenzene through non‐covalent interactions.     

Highly stable self-assembly in water: ion pair driven dimerization of a guanidiniocarbonyl pyrrole carboxylate zwitterion

The synthesis of a novel water-soluble guanidiniocarbonyl pyrrole carboxylate zwitterion 2 is described, and its self-association in aqueous solutions is studied. Zwitterion 2 forms extremely stable 1:1 dimers which are held together by an extensive hydrogen bonding network in combination with two mutual interacting ion pairs as could be shown by ESI MS and X-ray structure determination. NMR dilution studies in different highly polar solvents showed that dimerization is fast on the NMR time scale with association constants ranging from an estimated 10(10) M(-1) in DMSO to a surprisingly high 170 M(-1) in water. Hence, zwitterion 2 belongs to the most efficient self-assembling systems solely on the basis of electrostatic interactions reported so far. Furthermore, an amidopyridine pyrrole carboxylic acid 10 was developed as a neutral analogue of zwitterion 2, which also dimerizes with an essentially identical hydrogen bonding pattern (according to ESI MS and X-ray structure determination) but lacking the ionic interactions. NMR binding studies demonstrated that the solely hydrogen-bonded neutral dimer of 10 is stable only in organic solvents of low polarity (K > 10(4) M(-1) in CDCl3 but <10 M(-1) in 5% DMSO in CDCl3). The comparison of both systems impressively underlines the importance of ion pair interactions for stable self-association of such H-bonded binding motifs in water.     

Anion-pi-pi interactions in a dinuclear M2L2 metallocycle

The combination of the square-planar cis-protected [Pt(dppp)(O 3SCF 3) 2] (M) with the ditopic N, N'-bis(3,5-dimethyl-4-pyridinyl)-4-ethoxy-2,6-pyridinedicarboxamide ligand (L) leads both in solution and in the solid state to the quantitative self-assembly of a M 2L 2 metallocycle. We also report crystallographic evidence derived from the solid-state structure of the dinuclear metallocycle in support of the existence of anion-pi-pi interactions.     

Hybrid Organic–Inorganic Rotaxanes,Including a Hetero‐Hybrid [3]Rotaxane Featuring Two Distinct Heterometallic Rings and a Molecular Shuttle

[2] and [3] hybrid rotaxanes are reported based on {Ti₇M} rings (M is a trivalent metal such as Fe^III or Ga^III). NMR studies show that [2]rotaxanes can act as molecular shuttles, while EPR studies of [3]rotaxanes show weak interactions between the paramagnetic components of the supramolecular assemblies.     

Hybrid Organic–Inorganic Rotaxanes,Including a Hetero‐Hybrid [3]Rotaxane Featuring Two Distinct Heterometallic Rings and a Molecular Shuttle

[2] and [3] hybrid rotaxanes are reported based on {Ti₇M} rings (M is a trivalent metal such as Fe^III or Ga^III). NMR studies show that [2]rotaxanes can act as molecular shuttles, while EPR studies of [3]rotaxanes show weak interactions between the paramagnetic components of the supramolecular assemblies.     

Building a bridge between coordination compounds and clusters: bonding analysis of the icosahedral molecules [M(ER)12] (M = Cr, Mo, W; E = Zn, Cd, Hg)

The bonding situation of the icosahedral compounds [M(EH)(12)] (M = Cr, Mo, W; E = Zn, Cd, Hg), which are model systems for the isolated species [Mo(ZnCp*)(3)(ZnMe)(9)] possessing the coordination number 12 at the central atom M, have been analyzed with a variety of charge and energy decomposition methods (AIM, EDA-NOCV, WBI, MO). The results give a coherent picture of the electronic structure and the nature of the interatomic interactions. The compounds [M(EH)(12)] are transition metal complexes that possess 12 M-EH radial bond paths (AIM) that can be described as 6 three-center two-electron bonds (MO). The radial M-EH bonds come from the electron sharing interactions mainly between the singly occupied valence s and d AOs of the central atom M and the singly occupied EH valence orbitals (MO, EDA-NOCV). The orbital interactions provide ~42% of the total attraction, while the electrostatic attraction contributes ~58% to the metal-ligand bonding (EDA-NOCV). There is a weak peripheral E-E bonding in [M(EH)(12)] that explains the unusually high coordination number (MO). The peripheral bonding leads for some compounds [M(EH)(12)] to the emergence of E-E bond paths, while in others it does not (AIM). The relative strength of the radial and peripheral bonding in [Al(13)](-) and [Pt@Pb(12)](2-) is clearly different from the situation in [M(EH)(12)], which supports the assignments of the former species as cluster compounds or inclusion compounds (MO, WBI). The bonding situation in [WAu(12)] is similar to that in [M(EH)(12)].     

A computational study on the reactivity enhancement in the free radical polymerization of alkyl α‐hydroxymethacrylate and acrylate derivatives

The free radical polimerizability behavior of alkyl α‐hydroxymethacrylate (RHMA) derivatives ( M1–M3 ) has been modeled by considering the propagation of the dimeric units of the compounds of interest. All the transition structures in this class of monomers are stabilized by long‐range C?O…H? C interactions. The RHMA monomer bearing the ester functionality ( M2 ) polymerizes slightly faster than the one with the ether functionality ( M1 ) because of stronger electrostatic interactions between the C?O and H? C groups. 2‐(Methoxycarbonyl)allyl benzoate ( M3 ) shows higher reactivity as compared to M1 and M2 due to stronger electrostatic interactions. The same type of study has been carried out for hexyl ( M4 ), benzyl ( M5 ), and phenyl ( M6 ) acrylate derivatives whose increasing reactivity has been attributed to the presence of C?O…H? C, C?O…H‐? as well as π–π stabilizing interactions, respectively. While B3LYP/6‐31+G(d) has been used to locate the stationary points along the free radical polymerization of nonaromatic species, long‐range stabilizing interactions have only been detected with M06‐2X/6‐31+G(d). The kinetics that we obtain with this latter methodology for the free radical polymerization reactions of M1 – M6 agree well qualitatively with experiment. An implicit solvent model has reproduced the kinetics of M1–M3 in benzene the best. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013     

乙酰胆碱酯酶AChE与1,7-二氮杂咔唑抑制剂的作用机理的分子动力学模拟

通过分子对接、分子动力学(MD)模拟以及成键自由能分析方法,从原子水平上模拟研究了3种1,7-二氮杂咔唑衍生物(分别记为M1、M2和M3)与ACh E的结合模式及相互作用机理,分析和讨论了研究体系的静电相互作用和范德华相互作用(vd W)。用MM-PBSA方法计算的3种抑制剂与ACh E之间的结合自由能与抑制剂的实验生物活性数据(IC50值)相对应。分析结果表明,残基S286与抑制剂之间形成的氢键作用有利于抑制剂与ACh E之间的结合。范德华相互作用,尤其是抑制剂与关键残基W279和Y334的作用,对抑制剂与ACh E之间的结合自由能有较大的贡献,在区分抑制剂M1(或M2)和M3的生物活性上发挥着重要的作用。     

Noncovalent interactions in supramolecular complexes: a study on corannulene and the double concave buckycatcher

Stimulated by the recent observation of pi-pi interactions between C60 and corannulene subunits in a molecular tweezer arrangement (J Am Chem Soc 2007, 129, 3842), a density functional theory study was performed to analyze the electronic structure and properties of various noncovalent corannulene complexes. The theoretical approach is first applied to corannulene complexes with a series of benchmark molecules (CH4, NH3, and H2O) using several new-generation density functionals. The performance of nine density functionals, illustrated by computing binding energies of the corannulene complexes, demonstrates that Zhao and Truhlar's MPWB1K and M05-2X functionals provide energies similar to that obtained at the SCS-MP2 level. In contrast, most of the other popular density functionals fail to describe this noncovalent interaction or yield purely repulsive interactions. Further investigations with the M05-2X functional show that the binding energy of C60 with corannulene subunits in the relaxed molecular receptor clip geometry is -20.67 kcal/mol. The results of this calculation further support the experimental interpretation of pure pi-pi interactions between a convex fullerene and the concave surfaces of two corannulene subunits.     

Magnetic Anisotropy in a Family of Experimentally Synthesized and Theoretically Modeled M′6M8(CN24) Systems

A theoretical density functional study of the magnetic coupling interactions and magnetic anisotropy in a family of experimentally synthesized and theoretically modeled M′₆M₈(CN₂₄) (M′=Cu^II, Ni^II or Co^II; M=Fe^III or Cr^III) systems is presented. The calculations show that the interactions in the selected M′₆M₈(CN₂₄) are all ferromagnetic and the near cubic symmetry of Cu₆Fe₈ is the origin of its negative magnetic anisotropy parameter D.     

Solvent effects and hydration of a tripeptide in sodium halide aqueous solutions: an in silico study

In this work we are trying to gain insight into the mechanisms of ion-protein interactions in aqueous media at the molecular scale through fully atomistic molecular dynamics simulations. We present a systematic molecular simulation study of interactions of sodium and halide ions with a trialanine peptide in aqueous sodium halide solutions with different salts concentrations (0.20, 0.50, 1.0 and 2.0 M). Each simulation covers more than fifty nanoseconds to ensure the convergence of the results and to enable a proper determination of the tripeptide-ion interactions through the potentials of mean force. Changes in ion densities in the vicinity of different peptide groups are analysed and implications for the tripeptide conformations are discussed.     

A quantum chemical study of the interactions of uracil as a constituent of ribonucleic acid (RNA) with thiazolidinedione and rhodanine bioactive molecules: an insight into energetic and structural features

In this study, the biologically active configurations composed of Thiazolidinedione–Uracil (TU) and Rhodanine–Uracil (RU) have been fully investigated from the energetic and structural points of view, employing B3LYP and M062X functionals in combination with the different basis sets. Dispersion corrections to the interaction energy using M062X–GD3 and double hybrid density functionals (B2PLYP–GD2, B2PLYP–GD3 and mPW2PLYP–GD2) are also taking into account. The basis set superposition error-corrected interaction energy for hydrogen bonded configurations ranges from ??5.27 to ??13.53 and ??5.25 to ??12.93 kcal/mol for TU and RU complexes respectively as calculated at M062X/6–311++G(df,pd) level. The charge transfer process within all of the TU and RU configurations were analyzed using Natural Bond Orbital (NBO) calculations. The nature of the interactions is analyzed with NBO and Atoms in Molecules (AIM) analysis at M062X/6–311++G(df,pd) and energy decomposition analysis at BP86–D3/TZ2P(ZORA)//M062X/6–311++G(df,pd) level of theory. The results confirm that the nature of the interactions is nearly electrostatic, with a contribution of about 51–56% of the total interaction energy. The orbital interactions (ΔE_orb) for the considered TU and RU complexes have a contribution of about 24–38% of the total interaction energy. Based on the AIM and NBO results, the interactions were defined as electrostatic H-bonds with partially covalent character. In addition, correlation between interaction energies and vibrational frequency changes was investigated.     

乙酰胆碱酯酶AChE与1,7-二氮杂咔唑抑制剂的作用机理的分子动力学模拟

通过分子对接、分子动力学（MD）模拟以及成键自由能分析方法,从原子水平上模拟研究了3种1,7-二氮杂咔唑衍生物（分别记为M1、M2和M3）与AChE的结合模式及相互作用机理,分析和讨论了研究体系的静电相互作用和范德华相互作用（vdW）。用MM-PBSA方法计算的3种抑制剂与AChE之间的结合自由能与抑制剂的实验生物活性数据（IC₅₀值）相对应。分析结果表明,残基S286与抑制剂之间形成的氢键作用有利于抑制剂与AChE之间的结合。范德华相互作用,尤其是抑制剂与关键残基W279和Y334的作用,对抑制剂与AChE之间的结合自由能有较大的贡献,在区分抑制剂M1（或M2）和M3的生物活性上发挥着重要的作用。     

M(III)(bpym)(CN)(4)](-): a suitable building block to design ferrimagnetic cyano-bridged heterobimetallic chains (M = Fe, Cr; bpym = 2,2'-bypyrimidine)

Two cyano-bridged M(III)Mn(III) [M = Fe () and Cr ()] ferrimagnetic chains are reported; exhibits metamagnetism with two critical fields of 1250 G and 2.0 T which correspond to the overcoming by the applied dc field of the inter- and intrachain magnetic interactions, respectively.     

Nanodrop of an Ising magnetic fluid on a solid surface

The density functional theory of inhomogeneous simple fluids is extended to an Ising magnetic fluid in contact with a solid surface, which is subjected to an external uniform or nonuniform magnetic field. The system is described by two coupled integral equations regarding the magnetic moment and fluid density distributions. The dependence of the contact angle that a nanodrop makes with the solid surface on the parameters involved in the magnetic interactions between the molecules of fluid and between the molecules of fluid and an external magnetic field is calculated. For the uniform magnetic field, the contact angle increases with increasing magnetic field, approaching an asymptotic value that depends on the strength of the fluid-fluid magnetic interactions. In the nonuniform field generated by a permanent magnet, the contact angle first increases with increasing magnetic field B(M) and then decreases, with the decrease being almost linear for large values of B(M). The obtained results are in qualitative agreement with the experimental data on the contact angle of magnetic drops on a solid surface available in the literature.     

Phase transitions in DNA-linked nanoparticle assemblies: a decorated-lattice model

We use decorated-lattice models to explore the phase behavior of two types of DNA-linked colloidal mixtures: systems with identical nanoparticles functionalized with two different DNA strands (mixture Aab) and mixtures involving two types of particles each one functionalized with a different DNA strand (mixture Aa-Ab). The model allows us to derive the properties of the mixtures from the well-known behavior of underlying spin-n Ising models with temperature and activity dependent effective interactions. The predicted evolution of the dissolution profiles for the colloidal assemblies as a function of temperature and number of single DNA strands on a nanoparticle M is in qualitative agreement with that observed in real systems. According to our model, the temperature at which the assemblies dissolve can be expected to increase with increasing M only for concentrations of colloids below a certain threshold. For more concentrated solutions, the dissolution temperature is a decreasing function of M. Linker-mediated interactions between Aa and Ab particles in the Aa-Ab mixture render the phase separation involving disordered aggregates metastable with respect to a phase transition between a solvent-rich and an ordered phase. The stability of the DNA-linked assembly is enhanced by the ordering of the colloidal network and the ordered aggregates dissolve at higher temperatures. Our results may explain the contrasting evolution of the dissolution temperatures with increasing probe size in Aab and Aa-Ab mixtures as observed experimentally.