A scheme estimating the energy of intramolecular hydrogen bonds in diols

The relative energies of conformers of 1,2-ethanediol, 1,3-propanediol, and 1,4-butanediol are split into a sum of five different terms including the intramolecular OH?O interaction. This scheme allows to estimate the energy of the O-H?O intramolecular hydrogen bond of the tGG′g and gGG′g conformers of 1,3-propanediol, the g′GG′Gt and g′GG′Gg conformers of 1,4-butanediol, and the energy of the non-bonded O-H?O interaction in the g′Gt, g′Gg and g′Gg′ conformers of 1,2-ethanediol. This scheme provides pure hydrogen bond energies without assuming the geometry and/or electronic features to be constant between the conformation having a IHB and a reference conformation. The fitted energies show a perfect linear correlation with the corresponding r(H?O)⁻¹ values. QTAIM atomic electron population and energies of the donor hydrogen calculated along the H-O-C-C internal rotation are found to be linearly correlated. These linear correlations display small changes at the BCP formation in 1,3-propanediol.     

Hydrogen-Bonded and Halogen-Bonded: Orthogonal Interactions for the Chloride Anion of a Pyrazolium Salt

In the hydrochloride of a pyrazolyl-substituted acetylacetone, the chloride anion is hydrogen-bonded to the protonated pyrazolyl moiety. Equimolar co-crystallization with tetrafluorodiiodobenzene (TFDIB) leads to a supramolecular aggregate in which TFDIB is situated on a crystallographic center of inversion. The iodine atom in the asymmetric unit acts as halogen bond donor, and the chloride acceptor approaches the σ-hole of this TFDIB iodine subtending an almost linear halogen bond, with Cl···I = 3.1653(11) Å and Cl···I–C = 179.32(6)°. This contact is roughly orthogonal to the N–H···Cl hydrogen bond. An analysis of the electron density according to Bader’s Quantum Theory of Atoms in Molecules confirms bond critical points (bcps) for both short contacts, with ρbcp = 0.129 for the halogen and 0.321 eÅ−3 for the hydrogen bond. Our halogen-bonded adduct represents the prototype for a future class of co-crystals with tunable electron density distribution about the σ-hole contact.     

Natural bond orbital analysis: A critical overview of relationships to alternative bonding perspectives

We sketch the basic principles of natural bond orbital (NBO) theory, including critical discussion of its relationship to alternative bonding concepts and selected illustrations of its application to a broad spectrum of chemical bonding motifs. Particular emphasis is placed on the close NBO connections to prequantal bonding, and electromerism concepts, as well as the deep roots in quantal eigenvalue, superposition, and Pauli exclusion concepts that are manifested in many aspects of NBO donor–acceptor analysis. With respect to leading alternative perspectives, we identify similarities and differences that distinguish NBO theory from the corresponding precepts of valence bond theory, molecular orbital theory, and Bader's quantum theory of atoms in molecules, with critical discussion of the assumptions underlying characteristic differences in each case. © 2012 Wiley Periodicals, Inc.     

氢键对水杨酸酸度影响的量子化学研究

分子内氢键的形成影响羧酸的酸性,实验测定表明,水杨酸的酸性大约比苯甲酸强18倍,而其异构体——对羟基苯甲酸的酸性仅为苯甲酸的一半,已有文献从氢键形成角度定性讨论这一问题,我们采用CNDO/2法对其影响实质给予进一步的探讨,从微观角度阐述了该过程的可能机理,得到了与实验一致的结果。     

Theoretical investigation of C–HM interactions in organometallic complexes: A natural bond orbital (NBO) study

The nature of C–HM agostic interactions in model metal complexes [M²⁺(CH₂CH₃)(PH₃)_nCl] (where M = Sc, Ti, V, Ti, Cr, Mn, Fe, Co, Ni, Cu, Zn; n = 1, 2, 3, 4) was studied with the natural bond orbital analysis (NBO) approach using density functional theory (DFT) optimized geometries at the B3LYP/6-31G(d,p) level of theory. The effect of nature of metal, coordination number, oxidation state and ligand field effects on the agostic interaction is examined. A set of 20 crystal structures of organometallic complexes taken from the Cambridge Structural Database (CSD) was studied computationally employing AIM theory and NBO analysis, and the applicability of these methods was critically accessed in demarcating the two types of interaction.     

烷基咪唑型卤盐类离子液体的合成机理研究

用密度泛函理论考察了甲基咪唑和一系列的卤代烷烃(氯乙烷,氯丁烷,溴乙烷,溴丁烷)反应合成咪唑类离子液体的反应机理. 在B3LYP/6-31++G**//B3LYP/6-31G*基组水平上找到了两条反应路径：路径A(反应物→TS1→P1)和路径B(反应物→TS2→P2). 在路径A中, 卤素离子和咪唑环C2上的氢质子形成氢键；在路径B中, 卤素离子和咪唑环C5上的氢质子形成氢键. 计算发现, 氢键的形成在反应中起到了非常重要的作用, 特别是咪唑环C2上的氢质子在和卤素离子成氢键后形成了一个五员环结构的过渡态, 该过渡态能量较低. 经过渡态TS1的反应途径其活化能要低于经过渡态TS2的反应途径, 反应路径A为主要的反应通道. 计算结果表明, 经过渡态TS1的反应途径是一放热过程, 这和实验观察现象一致.     

DFT计算结合固体NMR研究富铝SSZ-13的铝分布和Br?nsted酸性

具有菱沸石(CHA)结构的SSZ-13分子筛在甲醇制烯烃(MTO)及柴油机车尾气氨选择性催化还原(NH_3-SCR)反应中具有重要的应用,采用富铝SSZ-13可以调节MTO反应的烯烃选择性和提升NH_3-SCR的低温脱硝活性,因此SSZ-13中的铝含量和分布与对应的酸性决定了其催化性能。本文采用密度泛函理论结合固体核磁共振实验研究了富铝和富硅HSSZ-13的Al位置与Br?nsted酸强度的内在关系。通过计算取代能发现,对于孤立Al位,质子位于Al周围4个不同O位时能量差异较小,最稳定的B酸位点是O(1)―H。对于富铝SSZ-13,两个Al原子位于同一六元环的对位是Al-Si-Si-Al (NNNN)序列中最稳定的结构,而Al-Si-Al (NNN)序列中能量最优的Al分布是两个铝原子排布于六棱柱上下不同的六元环上。通过计算最稳定构型下的质子亲和势、NH3脱附能和吸附氘代乙腈后的1H NMR化学位移,发现富铝SSZ-13中含有Si(2Al)分布的NNN序列导致了其Br?nsted酸强度弱于高硅的分子筛。分峰拟合29Si魔角旋转核磁共振(MASNMR)谱图表明富铝SSZ-13中Si(2Al)的含量在43%以上,而吸附氘代乙腈后的1H MAS NMR实验显示富铝SSZ-13的桥羟基化学位移向低场移动,进一步证明富铝SSZ-13具有较弱的Br?nsted酸强度。     

分子间弱相互作用的计算——构建氢键、卤键势能面

介绍一个面向大三下学期本科生的计算化学实验。通过量子化学计算对比研究两种分子间弱相互作用——氢键和卤键的势能面,使学生对势能面的概念及两种弱相互作用的区别有一定的直观认识。通过实际上机操作,初步了解Gaussian、Gaussview及Origin等计算化学相关软件的使用,并深入理解结构化学及计算化学课程中所学的理论知识。     

An efficient method for computing the QTAIM topology of a scalar field: The electron density case

An efficient method for computing the quantum theory of atoms in molecules (QTAIM) topology of the electron density (or other scalar field) is presented. A modified Newton–Raphson algorithm was implemented for finding the critical points (CP) of the electron density. Bond paths were constructed with the second‐order Runge–Kutta method. Vectorization of the present algorithm makes it to scale linearly with the system size. The parallel efficiency decreases with the number of processors (from 70% to 50%) with an average of 54%. The accuracy and performance of the method are demonstrated by computing the QTAIM topology of the electron density of a series of representative molecules. Our results show that our algorithm might allow to apply QTAIM analysis to large systems (carbon nanotubes, polymers, fullerenes) considered unreachable until now. © 2012 Wiley Periodicals, Inc.     

Assessing a double silicon decorated fullerene for the delivery of interacting flurbiprofen and salicylic acid drugs: A DFT approach

Since the number of drugs increases constantly, drug interactions appear as a critical issue to handle. The effective use of multiple drugs appears as another important subject to discuss and the use of targeted and selective delivery of drugs is becoming more important. Impurity doped C₆₀ fullerenes with various dopant atoms such as silicon or boron appear as promising drug delivery vehicles. Therefore, in the framework of this study, we investigated the interaction between salicylic acid and flurbiprofen and their controlled delivery by using double silicon decorated C₆₀ fullerene using density functional theory. Stability and reactivity considerations were also examined by investigating some important structural parameters, interaction energies and frontier molecular orbitals. The interactions were also monitored by examining important diagnostic vibrational bands. The strength of the interactions between atoms at the interaction sites was also identified by using the quantum theory of atoms in molecules.     

Forced Bonding and QTAIM Deficiencies: A Case Study of the Nature of Interactions in He@Adamantane and the Origin of the High Metastability

Calculations within the framework of the interacting quantum atoms (IQA) approach have shown that the interactions of the helium atom with both tertiary, tC, and secondary, sC, carbon atoms in the metastable He@adamantane (He@adam) endohedral complex are bonding in nature, whereas the earlier study performed within the framework of Bader’s quantum theory of atoms in molecules (QTAIM) revealed that only He???tC interactions are bonding. The He???tC and He???sC bonding interactions are shown to be forced by the high pressure that the helium and carbon atoms exert upon each other in He@adam. The occurrence of a bonding interaction between the helium and sC atoms, which are not linked by a bond path, clearly shows that the lack of a bond path between two atoms does not necessarily indicate the lack of a bonding interaction, as is asserted by QTAIM. IQA calculations showed that not only the destabilization of the adamantane cage, but also a huge internal destabilization of the helium atom, contribute to the metastability of He@adam, these contributions being roughly equal. This result disproves previous opinions based on QTAIM analysis that only the destabilization of the adamantane cage accounts for the endothermicity of He@adam. Also, it was found that there is no homeomorphism of the ρ( r ) and ‐v( r ) fields of He@adam. Comparison of the IQA and QTAIM results on the interactions in He@adam exposes other deficiencies of the QTAIM approach. The reasons for the deficiencies in the QTAIM approach are analyzed.     

Computational Study on the Mechanism of the Photouncaging Reaction of Vemurafenib: Toward an Enhanced Photoprotection Approach for Photosensitive Drugs

The photochemical behavior of the photosensitive first-line anticancer drug vemurafenib (VFB) is of great interest due to the impact of such behavior on its pharmacological activity. In this work, we computationally elucidated the mechanism of the photoinduced release of VFB from the 4,5-dimethoxy-2-nitrobenzene (DMNB) photoprotecting group by employing various density functional theory (DFT)/time-dependent DFT (TD-DFT) approaches. The computational investigations included a comparative assessment of the influence of the position of the photoprotecting group as a substituent on the thermodynamics and kinetics of the photouncaging reactions of two VFB-DMNB prodrugs, namely pyrrole (N_P) and sulfonamide (N_S). With the aid of the DFT calculations concerning the activation energy barrier (∆G^‡), the obtained results suggest that the step of the photoinduced intramolecular proton transfer of the DMNB moiety is not detrimental concerning the overall reaction profile of the photouncaging reaction of both prodrugs. However, the obtained results suggested that the position of the substitution position of the DMNB photoprotecting group within the prodrug structure has a substantial impact on the photouncaging reaction. In particular, the DMNB-N_s-VFB prodrug exhibited a notable increase in ∆G^‡ for the key step of ring opining within the DMNB moiety indicative of potentially hindered kinetics of the photouncaging process compared with DMNB-N_p-VFB. Such an increase in ∆G^‡ may be attributed to the electronic influence of the N_P fragment of the prodrug. The results reported herein elaborate on the mechanism of the photoinduced release of an important anticancer drug from photoprotecting groups with the aim of enhancing our understanding of the photochemical behavior of such photosensitive pharmaceutical materials at the molecular level.     

Density functional theory study of the free and tetraprotonated spheroidal macrotricyclic ligands and the complexes with halide anions: F−, Cl−, Br−

Theoretical studies of the macrotricyclic tetramine hexaether (SC), its tetraprotonated form SC‐4H⁺, and the corresponding complexes X^??SC‐4H⁺ (This expression represents the structural properties of the halide inclusion complex formed though the free ligand SC‐4H⁺ and the halide anion X^?: the spherical halide anion X^? is held by a tetrahedral array of ⁺N? H ··· X^? hydrogen bonds inside the intramolecular cavity of the tetraprotonated form SC‐4H⁺) of SC‐4H⁺ with the halide anions: F^?, Cl^?, and Br^? have been performed using density functional theory (DFT) with B3LYP/6‐31G method implemented in the Gaussian 03 program package. The optimized geometric structures obtained from DFT calculations are used to perform Natural Bond Orbital (NBO) analysis. The three main types of hydrogen bonds ⁺N? H ··· F^?, ⁺N? H ··· Cl^?, and ⁺N? H ··· Br^? are investigated. The results indicate that hydrogen bonding interactions are dominant and the halide anions: F^?, Cl^?, and Br^? offer lone pair electrons to the contacting σ* (N? H) antibond orbital of SC‐4H⁺. For all the structures, the most pronounced changes in geometric parameters upon interaction are observed in the proton‐donor molecule. The intermolecular interaction energies are predicted by using B3LYP/6‐31G methods with basis set superposition error (BSSE) and zero‐point energy (ZPE) correction. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

The Effect of Ge Incorporation on the Brønsted Acidity of ZSM‐5

The effect of the isomorphous substitution of some of the Si atoms in ZSM‐5 by Ge atoms on the Brønsted acid strength has been investigated by i) DFT calculations on cluster models of the formula ((HO)₃SiO)₃‐Al‐O(H)‐T‐(OSi(OH)₃)₃, with T=Si or Ge, and ((HO)₃SiO)₃‐Al‐O(H)‐Si‐(OGe(OH)₃)(OSi(OH)₃)₂, ii) a ³¹P NMR study of zeolite samples contacted with trimethyl phosphine oxide probe molecules and iii) a X‐ray photoelectron spectroscopy (XPS) study of ZSM‐5 and Ge‐ZSM‐5 samples. The calculations reveal that the effect of Ge incorporation on the framework acidity strongly depends on the degree of substitution and on the exact T‐atom positions that are occupied by Ge. High Ge concentrations allow for enhanced stabilisation of the deprotonated Ge‐ZSM‐5 through structural relaxation, resulting in a slightly higher acidity as compared to ZSM‐5. This structural relaxation is not achievable in Ge‐ZSM‐5 with a low Ge content, which therefore has a slightly lower acidity than ZSM‐5. The NMR study indicates no difference between the Brønsted acidity of ZSM‐5(47) and Ge(0.09)ZSM‐5(36). Instead, evidence for the presence of a substantial amount of Ge? OH groups in the Ge‐containing samples was obtained from the NMR results, which is consistent with earlier FTIR studies. The XPS results do not point to an effect of Ge on the framework acidity of ZSM‐5(47), instead, the results can be best interpreted by assuming the presence of additional Ge? OH and Si? OH groups near the surface of the Ge(0.08)ZSM‐5(47) sample.     

The Effect of Intramolecular Hydrogen Bond Type on the Gas-Phase Deprotonation of ortho-Substituted Benzenesulfonic Acids. A Density Functional Theory Study

Structural factors have been identified that determine the gas-phase acidity of ortho-substituted benzenesulfonic acid, 2-XC₆H₄–SO₃H, (X = –SO₃H, –COOH, –NO₂, –SO₂F, –C≡N, –NH₂, –CH₃, –OCH₃, –N(CH₃)₂, –OH). The DFT/B3LYP/cc-pVTZ method was used to perform conformational analysis and study the structural features of the molecular and deprotonated forms of these compounds. It has been shown that many of the conformers may contain anintramolecular hydrogen bond (IHB) between the sulfonic group and the substituent, and the sulfonic group can be an IHB donor or an acceptor. The Gibbs energies of gas-phase deprotonation Δ_rG⁰₂₉₈ (kJ mol^–1) were calculated for all compounds. It has been set that in ortho-substituted benzenesulfonic acids, the formation of various types of IHB is possible, having a significant effect on the Δ_rG⁰₂₉₈ values of gas-phase deprotonation. If the –SO₃H group is the IHB donor, then an ion without an IHB is formed upon deprotonation, and the deprotonation energy increases. If this group is an IHB acceptor, then a significant decrease in Δ_rG⁰₂₉₈ of gas-phase deprotonation is observed due to an increase in IHB strength and the A⁻ anion additional stabilization. A proton donor ability comparative characteristic of the –SO₃H group in the studied ortho-substituted benzenesulfonic acids is given, and the Δ_rG⁰₂₉₈ energies are compared with the corresponding values of ortho-substituted benzoic acids.     

Electronic and steric effects of substituents on the conformational diversity and hydrogen bonding of N-(4-X-phenyl)-N′,N″-bis(piperidinyl) phosphoric triamides (X = F, Cl, Br, H, CH3): A combined experimental and DFT study

Phosphoric triamides of the general formula (4-X-C₆H₄NH)P(O)(NC₅H₁₀)₂, X = F (1), Cl (2), Br (3), H (4) and CH₃ (5), have been synthesized and characterized. X-ray crystallography at 120 K reveals that the compounds 1, 3, 4·H₂O and 5 are composed of one, four, two and four conformers, respectively. DFT calculations were performed to investigate the electronic structures of the compounds. The X-ray data and DFT calculations revealed that the conformational diversity in these compounds is mainly governed by the steric effects of the substituent X rather than by electronic effects. Although substituent X does not participate directly in hydrogen bonding, the crystal packing of the compounds is influenced by the size of X. Atoms in molecules (AIM) and natural bond orbital (NBO) analyses confirm that the para substituent X has no significant effect on the electronic features of the amidic proton and the phosphoryl oxygen atom (O_P). Using X-ray crystallography, AIM and NBO analyses, the structural and electronic aspects of inter- and intramolecular hydrogen bonds of the compounds have been studied. The charge density (ρ) at the bond critical point (bcp) of the N-H bond decreases from the fully optimized monomers to their corresponding hydrogen bonded clusters. The N-H stretching frequency decreases from the calculated values to the experimental results.     

邻位甲基红水溶液的光谱性质随pH值的变化：含时密度泛函理论计算与实验研究

探明影响甲基红光谱性质的各种因素,有助于拓宽偶氮苯衍生物在有机光电器件中的应用。采用密度泛函理论和实验相结合的方法研究了溶液酸碱性和溶剂水对邻位甲基红水溶液光谱的影响。溶液pH从13.1逐渐降低至0.5,邻位甲基红水溶液的最大吸收波长从430 nm红移至520 nm。在不同酸碱条件下,主要有三种物种共存于甲基红水溶液中,它们分别是双质子化的甲基红o-H₂MR⁺ (强酸性条件下),单质子化的甲基红o-HMR (弱酸条件下)和碱性甲基红o-MR^- (碱性条件下),通过密度泛函理论计算研究了三种不同形式的电子结构特征。采用含时密度泛函理论计算了甲基红偶极跃迁允许的最低激发能,分别采用连续介质模型和分子簇模型研究水溶剂对甲基红电子结构和光谱性质的影响。在酸性条件下,o-H₂MR⁺和o-HMR分子内氢键导致π共轭体系平面性增强,因而光谱红移。而在碱性条件下,溶剂对o-MR^-的光谱有显著影响：极性o-HMR和o-MR^-与水分子的偶极-偶极相互作用导致光谱进一步红移。     

Halogen in materials design: Revealing the nature of hydrogen bonding and other non-covalent interactions in the polymorphic transformations of methylammonium lead tribromide perovskite

Methylammonium lead tribromide (CH₃NH₃PbBr₃) perovskite as a photovoltaic material has attracted a great deal of recent interest. Factors that are important in their application in optoelectronic devices include their fractional contribution of the composition of the materials as well as their microscopic arrangement that is responsible for the formation of well-defined macroscopic structures. CH₃NH₃PbBr₃ assumes different polymorphs (orthorhombic, tetragonal and cubic) depending on the evolution temperature of the bulk material. An understanding of the structure of these compounds will assist in rationalizing how halogen-centered non-covalent interactions play an important role in the rational design of these materials. Density functional theory (DFT) calculations have been performed on polymorphs of CH₃NH₃PbBr₃ to demonstrate that the H atoms on C of the methyl group in CH₃NH₃⁺ entrapped within a PbBr₆^4? perovskite cage are not electronically innocent, as is often contended. We show here that these H atoms are involved in attractive interactions with the surrounding bromides of corner-sharing PbBr₆^4? octahedra of the CH₃NH₃PbBr₃ cage to form Br?H(C) hydrogen bonding interactions. This is analogous to the way the H atoms on N of the NH₃⁺ group in CH₃NH₃⁺ form Br?H(N) hydrogen bonding interactions to stabilize the structure of CH₃NH₃PbBr₃. Both these hydrogen bonding interactions are shown to persist regardless of the nature of the three polymorphic forms of CH₃NH₃PbBr₃. These, together with the Br?C(N) carbon bonding, the Br?N(C) pnictogen bonding, and the Br?Br lump-hole type intermolecular non-covalent interactions identified for the first time in this study, are shown to be collectively responsible for the eventual emergence of the orthorhombic geometry of the CH₃NH₃PbBr₃ system. These conclusions are arrived at from a systematic analysis of the results obtained from combined DFT, Quantum Theory of Atoms in Molecules (QTAIM), and Reduced Density Gradient Non-Covalent Interaction (RDG-NCI) calculations carried out on the three temperature-dependent polymorphic geometries of CH₃NH₃PbBr₃.