Theoretical study of dihydrogen bonded clusters of water with tetrahydroborate

Ab initio calculations were used to analyze interactions of BH₄ ^? with 1?C4 molecules of H₂O at the MP2/6-311++G(d,p) and B3LYP/6-311++G(d,p) computational levels. The negative cooperativity for dihydrogen bond clusters containing H₂O···H₂O hydrogen bonds is more remarkable. The negative cooperativity is increased with increasing the size and also the number of hydrogen bonds in the cluster. The B?CH stretching frequencies show blue shifts with respect to cluster formation. Also greater blue shift of stretching frequencies where predicted for B?CH bonds which did not contribute in dihydrogen bonding with water molecules. The structures obtained have been analyzed with the Atoms in Molecules (AIM) methodology.     

Theoretical study and atoms in molecule analysis of hydrogen bonded clusters of ammonia and isocyanic acid

Abstract  

Ab initio and density functional calculations were used to analyze the interaction between a molecule of the isocyanic acid with 1 up to 4 molecules of ammonia at the B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) computational levels. The cooperative effect is increased with the increasing size of studied clusters. Red shifts of the H–N stretching frequency for complexes involving the isocyanic acid as an H-donor were predicted. Atom in molecules was used to analyze cooperative effects on topological parameters.     

A theoretical study on the mechanism and thermodynamics of ozone-water gas phase reaction

Ozone water reaction including a complex was studied at the MP2/6-311++G(d,p) and CCSD/6-311++G(2df,2p)//MP2/6-311++G(d,p) levels of theory. The interaction between water oxygen and central oxygen of ozone produces stable H₂O-O₃ complex with no barrier. With decomposition of this complex through H-abstraction by O₃ and O-abstraction by H₂O, three possible product channels were found. Intrinsic reaction coordinate, topological analyses of atom in molecule, and vibrational frequency calculation have been used to confirm the preferred mechanism. Thermodynamic data at T = 298.15 K and atmospheric pressure have been calculated. The results show that the production of hydrogen peroxide is the main reaction channel with ΔG = ?21.112 kJ mol^-1.     

Double resonance spectroscopy of different conformers of the neurotransmitter amphetamine and its clusters with water

In this paper the conformational landscape of amphetamine in the neutral ground state is examined by both spectroscopy and theory. Several spectroscopic methods are used: laser-induced fluorescence (LIF), resonance-enhanced two-photon ionization (R2PI), dispersed fluorescence and IR/R2PI hole burning spectroscopy. The latter two methods provide for the first time vibrationally resolved spectra of the neutral ground state of dl-amphetamine and the amphetamine–(H₂O)_1,2 complexes. Nine stable conformers of the monomer were found by DFT (B3LYP/6-311++G(d,p)) and ab initio (MP2/6-311++G(d,p)) calculations. For conformer analysis the vibrations observed in the IR/R2PI hole burning and dispersed fluorescence spectra obtained from single vibronic levels (SVLF) of a selected conformer were compared with the results of an ab initio normal mode analysis. By this procedure three S₀ → S₁ transitions in the R2PI spectrum were assigned to three different conformer structures. Another weak transition earlier attributed to another conformer could be assigned to a vibronic band of one of the three conformers. Furthermore spectra of amphetamine–(H₂O)_1,2 are tentatively assigned.     

FT-IR, FT-Raman vibrational spectra and molecular structure investigation of 2-chloro-4-methylaniline: A combined experimental and theoretical study

In this work, the experimental and theoretical vibrational spectra of 2-chloro-4-methylaniline (2Cl4MA, C₇H₈NCl) were studied. FT-IR and FT-Raman spectra of 2Cl4MA in the liquid phase have been recorded in the region 4000–400 cm⁻¹ and 3500–50 cm⁻¹, respectively. The structural and spectroscopic data of the molecule in the ground state have been calculated by using Hartree-Fock (HF) and density functional method (B3LYP) with the 6-31G(d), 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p) and 6-311G(d), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p) basis sets. The vibrational frequencies have been calculated and scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The DFT-B3LYP/6-311++G(d,p) calculations have been found more reliable than the ab initio HF/6-311++G(d,p) calculations for the vibrational study of 2Cl4MA. The optimized geometric parameters (bond lengths and bond angles) were compared with experimental values of aniline and p-methylaniline molecules.     

Theoretical study of hydrogen bonded clusters of water and fulminic acid

Ab initio and density functional calculations are used to analyze the interaction between a molecule of fulminic acid with 1, 2, 3, and 4 molecules of water along with a 2:2 complex at B3LYP/6-31+G(d,p) and MP2/6-311++G(d,p) computational levels. Cooperative effect (CE) in terms of stabilization energy of clusters are calculated and discussed as well. CE is increased with increasing cluster size of studied clusters. Red shifts of H–C stretching frequency for complexes involving HCNO as H-donor are predicted.     

The investigation on the relative stability of different clusters of thiourea dioxide in water using gas phase quantum chemical calculations

The relative stability of different clusters of thiourea dioxide (TDO) in water is examined using gas phase quantum chemical calculations at the MP2 and B3LYP level with 6‐311++G(d,p) basis set. The possible equilibrium structures and other energetic and geometrical data of the thiourea dioxide clusters, TDO‐(H₂O)_n (n is the number of water molecules), are obtained. The calculation results show that a strong interaction exists between thiourea dioxide and water molecules, as indicated by the binding energies of the TDO clusters progressively increased by adding water molecules. PCM model is used to investigate solvent effect of TDO. We obtained a negative hydration energy of ?20.6 kcal mol^?1 and free‐energy change of ?21.0 kcal mol^?1 in hydration process. On the basis of increasing binding energies with adding water molecules and a negative hydration energy by PCM calculation, we conclude thiourea dioxide can dissolve in water molecules. Furthermore, the increases of the C? S bond distance by the addition of water molecules show that the strength of the C? S bonds is attenuated. We find that when the number of water molecules was up to 5, the C? S bonds of the clusters, TDO‐(H₂O)₅ and TDO‐(H₂O)₆ were ruptured. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Synthesis, spectroscopic characterization, X-ray structure and DFT studies on 4-(2-hydroxyphenyl)-4,5,6,7-tetrahydro-1H-imidazo[4,5-c]pyridin-5-ium chloride hydrate

The title molecular salt, 4-(2-hydroxyphenyl)-4,5,6,7-tetrahydro-1H-imidazo[4,5-c]pyridin-5-ium chloride hydrate (C₁₂H₁₄N₃O⁺·Clˉ·H₂O), was synthesized and characterized by IR-NMR spectroscopy and single-crystal X-ray diffraction. In addition to the molecular geometry from X-ray experiment, the molecular geometry, vibrational frequencies and gauge-independent atomic orbital (GIAO) ¹H and ¹³C NMR chemical shift values of the title compound in the ground state have been calculated using the density functional theory (DFT/B3LYP) method with the 6-31++G(d,p) and 6-311++G(d,p) basis sets, and compared with the experimental data. Besides, molecular electrostatic potential (MEP) distribution and non-linear optical properties of the title compound were investigated by theoretical calculations at the B3LYP/6-311++G(d,p) level.     

The DFT study on mechanisms for NCO with C2H5 reaction

A detailed investigation has been performed at the QCISD(T)/6‐311++G(d,p)//B3LYP/6‐311+G(d,p) level for the reaction of NCO with C₂H₅ by constructing singlet and triplet potential energy surfaces (PES). The results show that the title reaction is more favorable on the singlet PES than on the triplet PES. On the singlet PES, the initial addition processes are barrierless and release lots of energy. The dominant channel occurs via the fragmentations of the initial adduct C₂H₅NCO and C₂H₅OCN to form C₂H₄ + HNCO and HOCN, respectively. With higher barrier heights, other products such as CH₄ + HNC + CO, CH₃CHNH + CO, CH₃CH + HNCO, and CH₃CN + H₂ + CO are less competitive. On the triplet PES, the entrance reactions surpass significant barriers; therefore, it could be negligible at the normal atmospheric condition. However, the most feasible channel on the triplet PES is the direct hydrogen abstraction channel to form CH₂CH₂ + HNCO. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Conformations of Serine in Aqueous Solutions as Revealed by Vibrational Circular Dichroism

Vibrational circular dichroism (VCD) spectroscopy is utilized to reveal the detailed conformational distributions of the dominant serine species in aqueous solutions under three representative pH conditions of 1.0, 5.7, and 13.0, together with vibrational absorption (VA) spectroscopy, density functional theory (DFT), and molecular dynamics simulation. The experimental VA and VCD spectra of serine in H₂O and D₂O in the fingerprint region under three pH values are obtained. DFT calculations at the B3LYP/6‐311++G(d,p) level are carried out for the protonated, zwitterionic, and deprotonated serine species. The lowest‐energy conformers of all three species are identified and their corresponding VA and VCD spectra simulated. A comparison between the gas‐phase simulations and the experimental VA and VCD spectra suggests that one or two of the most stable conformers of each species contribute predominantly to the observed data, although some discrepancies are noted. To account for the solvent effects, both the polarizable continuum model and the explicit solvation model are considered. Hydrogen‐bonded protonated, zwitterionic, and deprotonated serine–(water)₆ clusters are constructed based on radial distribution function analyses and molecular dynamics snapshots. Geometry optimization and VA and VCD simulations are performed for these clusters at the B3LYP/6‐311++G(d,p) level. Inclusion of the explicit water molecules is found to improve the agreement between theory and experiment noticeably in all three cases, thus enabling conclusive conformational distribution analyses of serine in aqueous solutions directly.     

Effects of Isomerization on the Measured Thermochemical Properties of Deprotonated Glycine/Protic‐Solvent Clusters

The thermochemical properties associated with the formation of an isomeric distribution of ROH???NH₂CH₂COO^? clusters (R=H, CH₃, C₂H₅) are measured by using high‐pressure mass spectrometry. A comparison of the measured properties with calculated values provides new insights into the thermochemical effects arising from the isomeric nature of this clustering system. When the distribution of isomers is correctly accounted for, the measured values of ΔH°, ΔS°, and ΔG°₂₉₈ consistently agree, to a very high degree of accuracy, with those predicted by MP2(full)/6‐311++G(d,p)//B3LYP/6‐311++G(d,p) calculations.     

Hydrogen-bonded clusters of hydroperoxyl radical with ammonia: a theoretical study

Ab initio calculations at MP2/6-311++G(d,p) computational level were used to analyze the interaction between a molecule of the hydroperoxyl radical with 1 up to 4 molecules of ammonia. Three minima were found for 1:2 and 1:4 complexes of HOO and NH₃. Two complexes were located as minima on the potential energy surface of 1:3 complexes. Red shifts of the OH stretching frequency upon complex formation in the range between 560 and 1,116 cm⁻¹ are predicted. Cooperative effect in terms of stabilization energy is calculated for the studied clusters. The cooperative effect is increased with the increasing size of studied clusters. The Quantum Theory Atoms in Molecules (QTAIM) theory was also applied to explain the nature of the complexes.     

DFT studies on the mechanism of the reaction of C2H5S with NO2

The mechanisms for the reaction of C₂H₅S with NO₂ are investigated at the QCISD(T)/6‐311++G(d, p)//B3LYP/6‐311++G(d, p) level on both single and triple potential energy surfaces. The geometries, vibrational frequencies and zero‐point energy (ZPE) corrections of all stationary points involved in the title reaction are calculated at the B3LYP/6‐311++G(d, p) level. The results show that the reaction is more predominant on the single potential energy surface, while it is negligible on the triple potential energy surface. Without barrier height in the whole process, the major channel is R → C₂H₅SONO (IM1 and IM2) → P1 (C₂H₅SO+NO). With much heat released in the formation of C₂H₅SNO₂ (IM3) and the transition state involved in the subsequent step more stable than reactants, P4 (CH₃CHS + t‐HONO) is subdominant product energetically. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

N2O…HOCl复合物结构和性质的理论研究

分别在DFT-B3LYP和MP2/6-311++G**水平上求得HOCl + N2O复合物势能面上的六种(S1, S2, S3, S4, S5和S6)和四种(S1, S2, S4和S5)构型. 频率分析表明,其中的S1和S3为过渡态,其它为稳定构型. 在复合物S3, S5 和S6中,HOCl 单体的σ*(5O-6H)作为质子供体,与N2O单体中作为质子受体的3O原子相互作用,形成氢键结构,而在氢键复合物S2中, 质子受体为N2O单体中的端1N原子;复合物S1中,HOCl分子的σ*(5O-4Cl)作为质子供体与N2O分子中的端1N原子(质子受体)相互作用,形成卤键结构,而复合物S4中的卤键结构的质子受体为N2O分子中的端3O原子. 经B3LYP/6-311++G**水平上的计算,考虑了基组重叠误差(BSSE)校正的单体间相互作用能在-1.56 ~ -8.73 kJ·mol-1之间. 采用自然键轨道理论(NBO)对两种单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了复合物中氢键和卤键键鞍点处的电子密度拓扑性质.     

乙醇-水分子团簇C2H5OH(H2O)n (n=1-9)稳定结构的量子化学研究

采用密度泛函理论B3LYP方法, 在B3LYP/6-311++G(2d,2p)//B3LYP/6-311++G(d,p)基组水平上对乙醇-水分子团簇(C₂H₅OH(H₂O)_n (n=1-9))的各种性质进行研究, 如: 优化的几何构型、结构参数、氢键、结合能、平均氢键强度、自然键轨道(NBO)电荷分布、团簇的生长规律等. 结果表明, 从二维(2-D)环状结构到三维(3-D)笼状结构的过渡出现在n=5的乙醇-水分子团簇中. 此外, 利用团簇结合能的二阶差分、形成能、能隙等性质, 发现在n=6时乙醇-水分子团簇的最低能量结构稳定性较好, 可能为幻数结构. 最后, 为了进一步探讨氢键本质, 将C₂H₅OH(H₂O)_n (n=2-9)最低能量结构的各种性质与纯水分子团簇(H₂O)_n (n=3-10)比较, 结果表明前者与后者中的水分子之间氢键相似.     

The phonon-assisted proton transfer between hydrazinium cations in (N2H5)2HMF6·2H2O (M∈{Ga, Al, Fe}) type compounds. FT IR and quantum theoretical study

FT IR spectra of a series of compounds with a general formula (N₂H₅)₂HMF₆·2H₂O (where M∈{Ga, Al, Fe}) were recorded at variable temperatures (from ∼100 to 300 K, at 10 K intervals). The appearance of the spectral region of ν(N-N) modes due to hydrazinium cations further supports the conclusions regarding the N₂H₅⁺?H⁺?N₂H₅⁺ hydrogen bond potential well based on Raman spectroscopic data [J. Raman Spectrosc. 28 (1997) 315]. The appearance of two bands corresponding to the ν(N-N) modes in the low temperature FT IR spectra that merge into one upon heating is a clear evidence of a symmetric potential well through which a phonon-assisted proton transfer (PAPT) occurs at higher temperatures. Ab initio MP2/6-311++G(2d,p) quantum chemical study of the proton transfer potential within the N₂H₅⁺?H⁺?N₂H₅⁺ cluster confirmed its double-minimum character. The first-order saddle point found on the MP2/6-311++G(2d,p) potential energy hypersurface corresponds to a centrosymmetric structure (C_2h symmetry), with the proton placed at the inversion center. The potential energy curve along the tunnelling coordinate was calculated by the intrinsic reaction coordinate (IRC) methodology, leading to an adiabatic PT barrier height of 3.94 kcal mol⁻¹ and a tunneling rate of 1.98 s⁻¹. The corresponding MP4(SDTQ)/6-311++G(2d,p)//MP2/6-311++G(2d,p) value of the adiabatic PT barrier height is 4.26 kcal mol⁻¹.     

X-ray diffraction and vibrational spectroscopic studies of indolecarboxylic acids and their metal complexes: Part VII. Indole-2-carboxylic acid and catena-poly[[diaquazinc(II)]-bis(μ2-indole-2-carboxylato-O:O′)]

The catena-poly[[diaquazinc(II)]-bis(μ²-indole-2-carboxylato-O:O′)], [Zn(I2CA)₂(H₂O)₂]_n has been synthesized and characterized by X-ray diffraction analysis and the infrared and Raman spectroscopic methods. The co-ordination of the indole-2-carboxylate anion to Zn(II) results in the formation of the [Zn(I2CA)₂(H₂O)₂]_n, in which the Zn(II) cations lie on inversion centres in space group P2_1/c, with water ligands in the apical sites of octahedral geometry. Moreover, the infrared and Raman spectra of indole-2-carboxylic acid (I2CA) and the infrared spectrum of deuterated derivative of indole-2-carbocylic acid (I2CA-d2) are recorded in the solid phase. The theoretical wavenumbers, infrared intensities and Raman scattering activities were calculated by density functional B3LYP and mPW1PW91 methods with the 6-311++G(d,p) basis set for I2CA and I2CA-d2 and with the 6-311++G(d,p)/LanL2DZ basis sets for the theoretical model of Zn(I2CA)₂(H₂O)₂]_n. The detailed vibrational assignment has been made on the basis of the calculated potential energy distribution for all molecules.     

Theoretical studies of uracil–(H2O)n (n = 1–7) clusters by ab initio and ABEEMσπ/MM fluctuating charge model

Uracil–(H₂O)_n (n = 1–7) clusters were systemically investigated by ab initio methods and the newly constructed ABEEMσπ/MM fluctuating charge model. Water molecules have been gradually placed in an average plane containing uracil. The geometries of 38 uracil–water complexes were obtained using B3LYP/6-311++G** level optimizations, and the energies were determined at the MP2/6-311++G** level with BSSE corrections. The ABEEMσπ/MM potential model gives reasonable properties of these clusters when comparing with the present ab initio data. For interaction energies, the root mean square deviation is 0.96 kcal/mol, and the linear coefficient reaches 0.997. Furthermore, the ABEEMσπ charges changed when H₂O interacted with the uracil molecule, especially at the sites where the hydrogen bond form. These results show that the ABEEMσπ/MM model is fine giving the overall characteristic hydration properties of uracil–water systems in good agreement with the high-level ab initio calculations.     

Density functional investigations on the (H2O)n·CCH and (H2O)n·HCC complexes (n=1–3)

The electronic structures and energies of (H₂O)_n·CCH and (H₂O)_n·HCC complexes (n=1–3) between CCH and water have been theoretically investigated at the UB3LYP/6-311++G(2df,p)//UB3LYP/6-311G(d,p) level. The complexes with n=2–3 are cyclic structures with homodromic hydrogen-bond chain. The (H₂O)_n·CCH (n=1–3) complexes show increasing stabilities towards CCH- or H₂O-eliminations of 2.3, 5.8 and 7.6 kcal/mol and are energetically more stable than the corresponding (H₂O)_n·HCC complexes by 0.8, 2.7 and 3.4 kcal/mol, respectively, due to the charge-separation-enhanced hydrogen bonds within (H₂O)_n·CCH (n=2,3). Strong interactions between CCH and (H₂O)₂ and (H₂O)₃ clusters suggest special solvent effects of water on the chemical behavior of unsaturated radicals.     

Supramolecular study,Hirshfeld analysis and theoretical study of 6‐methoxyquinoline N‐oxide dihydrate

In the crystal structure of 6‐methoxyquinoline N‐oxide dihydrate, C₁₀H₉NO₂·2H₂O, (I), the presence of two‐dimensional water networks is analysed. The water molecules form unusual water channels, as well as two intersecting mutually perpendicular columns. In one of these channels, the O atom of the N‐oxide group acts as a bridge between the water molecules. The other channel is formed exclusively by water molecules. Confirmation of the molecular packing was performed through the analysis of Hirshfeld surfaces, and (I) is compared with other similar isoquinoline systems. Calculations of bond lengths and angles by the Hartree–Fock method or by density functional theory B3LYP, both with 6‐311++G(d,p) basis sets, are reported, together with the results of additional IR, UV–Vis and theoretical studies.