Bond Dipole Moments Research Articles

Electronic structures and chemical bonding in 4d- and 5d-transition metal mononitrides

Bond distances, vibrational frequencies, dipole moments, dissociation energies, electron affinities and ionisation potentials of 4d- and 5d- transition metal mononitrides molecules in neutral, positively and negatively charged ions were studied using density functional method B3LYP. The bonding patterns are complex for these systems, which involves covalent, ionic and dative components. The calculated results are compared with the available data and across the series.

Molecular structure and electronic spectrum of CaS under electric fields

The method B3LYP of the density functional theory （DFT） at 6-311++G（d, p） level has been used to obtain equilibrium structure of the ground state of CaS molecule, optimized parameters, dipole moment, charge distribution, HOMO energy level, LUMO energy level, energy gaps, infrared spectrum and harmonic frequency under different external electric fields ranging from -0.03 a.u. to 0.045 a.u. The results shows that with increasing the external electric field, the molecular geometry becomes strongly dependent on the field strength and behaves asymmetrically to the direction of the applied electric field. At the same time, the bond length and dipole moment μ of the ground state are changed from decreasing to increasing. At F=0.02 a.u., the minimum of bond length and dipole moment are 0.2289 nm and 1.5969 D. HOMO energy level and LUMO energy level are changed from increasing to decreasing. A decrease of the total energy gaps are found in the process of increasing the external electric field, which tells that the molecule is excited easily under a specific electric field. Excitation energies and oscillator strengths are affected by the external electric field. These results are useful for the study on the electroluminescence of CaS molecule.

Ultrasonic and DFT study of intermolecular association through hydrogen bonding in aqueous solutions of d(−)-arabinose

The experimental measurements of density, viscosity and ultrasonic velocity of aqueous d-arabinose solutions were carried out as functions of concentration (0.1 ≤ m [mol kg − 1 ] ≤ 1.0) and temperature (303.15 ≤ T [K] ≤ 323.15). The isentropic compressibility ( β s), acoustic impedance ( Z), hydration number ( H n), intermolecular free length ( L f), classical sound absorption ( α/ f 2) class and shear relaxation time ( τ) were calculated by using the measured data. These parameters have been interpreted in terms of solute–solvent interactions. The quantum chemical calculations were performed to study the hydrogen bonding in interacting complex formed between α-D-arabinopyranose in 1C 4 conformation and water molecules. Computations have been done by using Density Functional Theory (DFT) method at B3LYP/6-31+g(d) level of theory to study the equilibrium structure of α- d-arabinose, α-D-arabinopyranose–water interacting complex and vibrational frequencies. The solution phase study was carried out using Onsager's reaction field model in water solvent. The computed and scaled vibrational frequencies are in good agreement with the main features of the experimental spectrum when seven water molecules are considered explicitly with α-D-arabinopyranose in 1C 4 conformation. The interaction energy ( E total), hydrogen bond lengths and dipole moment ( μ m) of the interacting complex are also presented and discussed with in the light of solute–solvent interactions.

A New Proposal for the Ground State of the FeO− Cluster in the Gas Phase and for the Assignment of Its Photoelectron Spectra

High-level multireference CASPT2 calculations are performed to determine the electronic structures of the FeO and FeO(-) clusters. Geometry optimizations of all possible low-lying states of the two unsaturated complexes are carried out at the mentioned theoretical level by calculating their potential energy curves. FeO(-) is proposed to possess a (6)Sigma(+) ground state as opposed to the (4)Delta state, which has been put forward as the ground state by previous computational studies. On this basis an alternative assignment of the photoelectron spectra of this anion is postulated. All features of these spectra are tentatively attributed to either septet or quintet states of the neutral FeO cluster. The lowest energy band in the spectra is then the result of electron detachments to the (5)Delta ground state and the (5)Sigma(+) lowest excited state. The second lowest band might be due to the (7)Sigma(+). Two higher energy bands are thought to originate from two (5)Pi states and a (5)Phi. Vibrational progressions that are observed for some bands could be explained in terms of the calculated potential energy profiles of the relevant states. Credibility for the proposed assignment is rendered by the good correspondence between experiment and our computational method concerning the bond distance and dipole moment for the ground state of FeO.

EaMEAD: Activation Energy Prediction of Cytochrome P450 Mediated Metabolism with Effective Atomic Descriptors

In an effort to improve drug design and predictions for pharmacokinetics (PK), an empirical model was developed to predict the activation energies (Ea) of cytochrome P450 (CYP450) mediated metabolism. The model, EaMEAD (Activation energy of Metabolism reactions with Effective Atomic Descriptors), predicts the Ea of four major metabolic reactions of the CYP450 enzyme: aliphatic hydroxylation, N-dealkylation, O-dealkylation, and aromatic hydroxylation. To build and validate the empirical model, the E(a) values of the substrates with diverse chemical structures (394 metabolic sites for aliphatic hydroxylation, 27 metabolic sites for N-dealkylation, 9 metabolic sites for O-dealkylation, and 85 metabolic sites for aromatic hydroxylation) were calculated by AM1 molecular orbital (MO). Empirical equations, Quantitative Structure Activity Relationship (QSAR) models, were derived using effective atomic charge, effective atomic polarizability, and bond dipole moments of the substrates as descriptors. EaMEAD is shown to accurately predict Ea with a correlation coefficient (R) of 0.94 and root-mean-square error (RMSE, unit is kcal/mol) of 0.70 for aliphatic hydroxylation, N-dealkylation, and O-dealkylation, and R of 0.83 and RMSE of 0.80 for aromatic hydroxylation, respectively. Physical origin and the role of the effective atomic descriptors of the models are presented in detail. With this model, the Ea of the metabolism can be rapidly predicted without any experimental parameters or time-consuming QM calculation. Regioselectivity prediction with our model is presented in the case of CYP3A4 metabolism. The reliability and ease of use of this model will greatly facilitate early stage PK predictions and rational drug design. Moreover, the model can be applied to develop the Ea prediction model of various types of chemical reactions.

Chemical Bonding and Electronic Structure of 4d-Metal Monosulfides

Bond distances, vibrational frequencies, dissociation energies, electron affinities, ionization potentials and dipole moments of the title molecules in neutral and charged ions were studied by use of density functional method. Ground states for each molecule were assigned. The calculated bond distance decreases with the increasing of atomic number of 4d metals, reaches minimum at RhS, then increases. For cationic molecules, the calculated bond distance decreases to the minimum at MoS+, then increases. The calculated vibrational frequency decreases from YS(YS+) to PdS(PdS+) for both neutral and cationic molecules. The bond ionic character decreases from YS(YS+) to PdS(PdS+) for neutral and cationic molecules. The bonding patterns are discussed and compared with the available studies.

Synthesis and Quantitative Structure−Antifungal Activity Relationships of Clovane Derivatives against Botrytis cinerea

Twenty-three clovane derivatives, nine described here for the first time, bearing substituents on carbon C-2, have been synthesized and evaluated for their in vitro antifungal activity against the phytopathogenic fungus Botrytis cinerea. The results showed that compounds 9, 14, 16, and 18 bearing nitrogen atoms in the chain attached at C-2 displayed potent antifungal activity, whereas mercapto derivatives 13, 19, and 22 displayed low activity. The antifungal activity showed a clear structure-activity relationship (SAR) trend, which confirmed the importance of the nature of the C-2 chain on the antifungal activity. On the basis of these observations, the metabolism of compounds 8 and 14 by the fungus B. cinerea, and the metabolism of other clovanes by this fungus, described previously, a pro-drug action mechanism for 2-alkoxyclovane compounds is proposed. Quantitative structure-activity relationship (QSAR) studies were performed to rationalize the results and to suggest further optimization, using a topological sub-structural molecular design (TOPS-MODE) approach. The model displayed good fit and predictive capability, describing 85.5% of the experimental variance, with a standard deviation of 9.502 and yielding high values of cross-validation determination coefficients (q2CV-LOO = 0.784 and q2boot = 0.673). The most significant variables were the spectral moments weighted by bond dipole moment (Dip), hydrophobicity (Hyd), and the combined dipolarity/polarizability Abraham molecular descriptor (Ab-pi2H).

Solvation in Pure Liquids: What Can Be Learned from the Use of Pairs of Indicators?

The solvation of six solvatochromic probes in a large number of solvents (33-68) was examined at 25 degrees C. The probes employed were the following: 2,6-diphenyl-4-(2,4,6-triphenylpyridinium-1-yl) phenolate (RB); 4-[(E)2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePM; 1-methylquinolinium-8-olate, QB; 2-bromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePMBr, 2,6-dichloro-4-(2,4,6-triphenyl pyridinium-1-yl) phenolate (WB); and 2,6-dibromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePMBr(2), respectively. Of these, MePMBr is a novel compound. They can be grouped in three pairs, each with similar pK(a) in water but with different molecular properties, for example, lipophilicity and dipole moment. These pairs are formed by RB and MePM; QB and MePMBr; WB and MePMBr(2), respectively. Theoretical calculations were carried out in order to calculate their physicochemical properties including bond lengths, dihedral angles, dipole moments, and wavelength of absorption of the intramolecular charge-transfer band in four solvents, water, methanol, acetone, and DMSO, respectively. The data calculated were in excellent agreement with available experimental data, for example, bond length and dihedral angles. This gives credence to the use of the calculated properties in explaining the solvatochromic behaviors observed. The dependence of an empirical solvent polarity scale E(T)(probe) in kcal/mol on the physicochemical properties of the solvent (acidity, basicity, and dipolarity/polarizability) and those of the probes (pK(a), and dipole moment) was analyzed by using known multiparameter solvation equations. For each pair of probes, values of E(T)(probe) (for example, E(T)(MePM) versus E(T)(RB)) were found to be linearly correlated with correlation coefficients, r, between 0.9548 and 0.9860. For the mercyanine series, the values of E(T)(probe) also correlated linearly, with (r) of 0.9772 (MePMBr versus MePM) and 0.9919 (MePMBr(2) versus MePM). The response of each pair of probes (of similar pK(a)) to solvent acidity is the same, provided that solute-solvent hydrogen-bonding is not seriously affected by steric crowding (as in case of RB). We show, for the first time, that the response to solvent dipolarity/polarizability is linearly correlated to the dipole moment of the probes. The successive introduction of bromine atoms in MePM (to give MePMBr, then MePMBr(2)) leads to the following linear decrease: pK(a) in water, length of the phenolate oxygen-carbon bond, length of the central ethylenic bond, susceptibility to solvent acidity, and susceptibility to solvent dipolarity/polarizability. Thus studying the solvation of probes whose molecular structures are varied systematically produces a wealth of information on the effect of solute structure on its solvation. The results of solvation of the present probes were employed in order to test the goodness of fit of two independent sets of solvent solvatochromic parameters.

Cooperativity between the Dihydrogen Bond and the N⋅⋅⋅HC Hydrogen Bond in LiH–(HCN)nComplexes

The cooperativity between the dihydrogen bond and the NHC hydrogen bond in LiH-(HCN)(n) (n=2 and 3) complexes is investigated at the MP2 level of theory. The bond lengths, dipole moments, and energies are analyzed. It is demonstrated that synergetic effects are present in the complexes. The cooperativity contribution of the dihydrogen bond is smaller than that of the NHC hydrogen bond. The three-body energy in systems involving different types of hydrogen bonds is larger than that in the same hydrogen-bonded systems. NBO analyses indicate that orbital interaction, charge transfer, and bond polarization are mainly responsible for the cooperativity between the two types of hydrogen bonds.

Structure of the Methanol Liquid−Vapor Interface: A Comprehensive Particle-Based Simulation Study

This research addresses a comprehensive particle-based simulation study of the structural, dynamic, and electronic properties of the liquid-vapor interface of methanol utilizing both ab initio (based on density functional theory) and empirical (fixed charge) models. Numerous properties such as interfacial width, hydrogen bond populations, dipole moments, and correlation times are characterized with identical schemes to draw useful conclusions on the strengths and weakness of the proposed models for the interface of neat methanol. Our findings indicate that all models considered in this study yield similar results for the radial distribution functions, hydrogen bond populations, and orientational relaxation times. Significant differences in the models appear when examining both the dipole moments and surface relaxation near the aqueous liquid-vapor interface. Here, the density functional theory interaction potential predicts a significant decrease in the molecular dipole moment and slight expansion in the oxygen-oxygen distance as the interface is approached. This work was supported by the U.S. Department of Energy's (DOE) Office of Basic Energy Sciences, Chemical Sciences program. The Pacific Northwest National Laboratory is operated by Battelle for DOE. For submission to Journal of Physical Chemistry B

Ultrasonic and DFT study of intermolecular association through hydrogen bonding in aqueous solutions of glycerol

The experimental measurements of density, viscosity and ultrasonic velocity of aqueous glycerol solutions were carried out as functions of concentration (0.1 ≤ m [mol kg − 1 ] ≤ 1.0) and temperature (303.15 ≤ T [K] ≤323.15). The isentropic compressibility ( β s ), acoustic impedance ( Z), hydration number ( H n), intermolecular free length ( L f), classical sound absorption ( α/ f 2) class and shear relaxation time ( τ) were calculated by using the measured data. These parameters have been interpreted in terms of solute–solvent interactions. The quantum chemical calculations were performed to study the hydrogen bonding in interacting complex formed between glycerol and water molecules. Computations have been done by using Density Functional Theory (DFT) method at B3LYP/6–31 + g(d) level of theory to study the equilibrium structure of glycerol, glycerol–water interacting complex and vibrational frequencies. The solution phase study was carried out using Onsager's reaction field model in water solvent. The computed vibrational frequencies are in good agreement with the main features of the experimental spectrum when four water molecules are considered explicitly with glycerol. The interaction energy ( E total), hydrogen bond lengths and dipole moment ( µ m) of the interacting complex are also presented and discussed with in the light of solute–solvent interactions.

Electronic structures and chemical bonding in 4d transition metal monohalides

Bond distances, vibrational frequencies, dipole moments, dissociation energies, electron affinities, and ionization potentials of MX (XM = Y-Cd, X = F, Cl, Br, I) molecules in neutral, positively, and negatively charged ions were studied by density functional method, B3LYP. The bonding patterns were analyzed and compared with both the available data and across the series. It was found that besides ionic component, covalent bonds are formed between the 4d transition metal s, d orbitals, and the p orbital of halogen. For both neutral and charged molecules, the fluorides have the shortest bond distance, iodides the longest. Although the opposite situation is observed for vibrational frequency, that is, fluorides have the largest value, iodides the smallest. For neutral and anionic species, the dissociation energy tends to decrease with the increasing atomic number from Y to Cd, suggesting the decreasing or weakening of the bond strength. For cationic species, the trend is observed from Y to Ag.

Calculations of bond dissociation energies and dipole moments in energetic materials using density-functional methods

We compare the effectiveness of six exchange/correlation functional combinations (Becke/Lee, Yang and Parr; Becke-3/Lee, Yang and Parr; Becke/Perdew–Wang 91; Becke-3/Perdew–Wang 91; Becke/Perdew 86; Becke-3/Perdew 86) for computing C–N, O–O and N–NO 2 dissociation energies and dipole moments of five compounds. The studied compounds are hexabydro-1,3,5-trinitro-1,3,5-triazine (RDX), dimethylnitramine, cyanogen, nitromethane and ozone. The Becke-3/Perdew 86 in conjunction with 6-31G** is found to give the best results, although for the dipole moments of RDX, there is a slightly difference that B3P86/6-31G** is less reliable than B3P86/6-31+G**.

Ultrasonic and computational study of intermolecular association through hydrogen bonding in aqueous solutions of d-mannitol

The estimation of density, viscosity and ultrasonic velocity of aqueous d-mannitol solutions was carried out as functions of concentration (0.1 ≤ m [mol kg − 1 ] ≤ 1.0) and temperature (303.15 ≤ T [K] ≤ 323.15). The adiabatic compressibility ( β ad), hydration number ( H n), internal pressure ( π i), classical sound absorption ( α/ f 2) class and shear relaxation time ( τ) were calculated through ultrasonic experimental method. These parameters have been interpreted in terms of solute–solvent interactions. The quantum chemical calculations were performed to study the hydrogen bonding in interacting complex formed between mannitol and water molecules. Computations have been done by using Density Functional Theory (DFT) method at B3LYP/6–31 + g( d) level of theory to study the equilibrium structure of mannitol, mannitol–water interacting complex and vibrational frequencies. The solution phase study was carried out using Onsager's reaction field model in water solvent. The computed vibrational frequencies are in good agreement with the main features of the experimental spectrum when eight water molecules are considered explicitly with the d-mannitol. The interaction energy ( E total), hydrogen bond lengths and dipole moment ( μ m) of the interacting complex were also presented and discussed within the light of solute–solvent interactions.

Density Functional Studies of Diatomic LaO to LuO

Bond distances, vibrational frequencies, electron affinities, ionization potentials, dissociation energies and dipole moments of the title molecules in neutral, positively and negatively charged ions were studied by use of density functional method. Ground electronic state was assigned for each molecule. The bonding patterns were analyzed and compared with both the available data and across the series. It was found that besides ionic component, covalent bonds are formed between the metal s, d and f orbitals and oxygen p orbitals. Contrary to the well known lanthanide contraction, the bond distance is not regular from LaO to LuO for both neutral and charged molecules. An obvious population at 5d orbital was observed through the lanthanide series. 4f electrons also participate the chemical bonding for CeO to NdO and TbO to TmO. For EuO, GdO, YbO and LuO, 4f electrons tend to be localized. The spin multiplicity is regular for neutral and charged molecules. The spin multiplicity of the charged molecules can be obtained by −1 (or +1 for TbO+, DyO+, YbO− and YbO+) compared with the corresponding neutral molecules.

Electronic structures and chemical bonding in diatomic ScX to ZnX (X = S, Se, Te)

Bond distances, vibrational frequencies, electron affinities, ionization potentials, dissociation energies, and dipole moments of the title molecules in neutral, positively, and negatively charged ions were studied using density functional method. Ground electronic state was assigned for each molecule. The bonding patterns were analyzed and compared with both the available data and across the series. It was found that, besides ionic component, covalent bonds are formed between the metal s, d orbitals, and the p orbital of S, Se, and Te. For neutral and cationic molecules, the covalent character increases from ScX to CrX and from FeX to CuX with an exception of decrease at MnX and ZnX, while for anionic molecules, the trend is not obvious. For both neutral and charged molecules, the sulfides have the shortest bond distance and largest vibrational frequency, while tellurides have the largest bond distance and smallest vibrational frequency. For neutral and anionic molecules, the dissociation energy of sulfides is the largest, that of tellurides is the smallest, while this only remains true for cationic molecules from ScX(+) to FeX(+).

Covalent versus ionic bonding in alkalimetal fluoride oligomers

The most polar bond in chemistry is that between a fluorine and an alkalimetal atom. Inspired by our recent finding that other polar bonds (C--M and H--M) have important covalent contributions (i.e., stabilization due to bond overlap), we herein address the question if covalency is also essential in the F--M bond. Thus, we have theoretically studied the alkalimetal fluoride monomers, FM, and (distorted) cubic tetramers, (FM)4, with M=Li, Na, K, and Rb, using density functional theory at the BP86/TZ2P level. Our objective is to determine how the structure and thermochemistry (e.g., F--M bond lengths and strengths, oligomerization energies, etc.) of alkalimetal fluorides depend on the metal atom, and to understand the emerging trends in terms of quantitative Kohn-Sham molecular orbital theory. The analyses confirm the extreme polarity of the F--M bond (dipole moment, Voronoi deformation density and Hirshfeld atomic charges), and they reveal that bond overlap-derived stabilization (ca. -6, -6, and -2 kcal/mol) contributes only little to the bond strength (-136, -112, and -114 kcal/mol) and the trend therein along Li, Na, and K. According to this and other criteria, the F--M bond is not only strongly polar, but also has a truly ionic bonding mechanism. Interestingly, the polarity is reduced on tetramerization. For the lithium and sodium fluoride tetramers, the F4 tetrahedron is larger than and surrounds the M4 cluster (i.e., F--F>>M--M). But in the potassium and rubidium fluoride tetramers, the F4 tetrahedron is smaller than and inside the M4 cluster (i.e., F--F<M--M).

Density functional theoretical (DFT) study for the prediction of spectroscopic parameters of ClCCCN

DFT(B3LYP, B3PW91) calculations in conjunction with three different basis sets have been utilized to investigate the variations in the bond lengths, dipole moment, rotational constants, IR frequencies, IR intensities and rotational invariants of ClCCCN. The nuclear quadrupole constants of chlorine (35Cl, 37Cl) and nitrogen (14N) of ClCCCN have been calculated on the experimental rs structure as well as on the B3PW91/6–311++g(d,p) optimized geometry and were found to be within the scale length of the experimental uncertainty. The slope and intercept obtained from the regression analysis between the B3LYP/6–311++g(d,p) level calculated and experimental Bo values of ClCCCN were used to calculate reasonable values of rotational constants of all the rare isotopic species of ClCCCN having standard deviation ±0.048MHz. All the spectroscopic parameters obtained from DFT calculations show satisfactory agreement with the available experimental data.

Chemical bonding and electronic structure of 4d-metal monocarbides

Bond distances, vibrational frequencies, dissociation energies, electron affinities, ionization potentials and dipole moments of the title molecules in neutral and charged ions were studied by use of density functional method. Ground states for each molecule were assigned. For neutral and cationic molecules, the bond distance decreases from YC (YC +) to RhC (RhC +), then increases, while for anionic molecules, the bond distance decreases from YC − to RuC −, then increases. Opposite trend was observed for vibrational frequency. The bond ionic character decreases from ZrC to PdC for neutral molecules. The bonding patterns are discussed and compared with the available studies.

Electronic structures and chemical bonding in transition metal monosilicides MSi (M=3d, 4d, 5d elements)

Bond distances, vibrational frequencies, electron affinities, ionization potentials, dissociation energies, and dipole moments of the title molecules in neutral, positively, and negatively charged ions were studied using the density functional method. Ground state was assigned for each species. The bonding patterns were analyzed and compared with both the available data and across the series. It was found that besides an ionic component, covalent bonds are formed between the metal s,d orbitals and the silicon 3p orbital. The covalent character increases from ScSi (YSi) to NiSi (PdSi) for 3d (4d) metal monosilicides, then decreases. For 5d metal monosilicides, the covalent character increases from LaSi to OsSi, then decreases. For the dissociation of cations, the dissociation channel depends on the magnitude of the ionization potential between metal and silicon. If the ionization potential of the metal is smaller than that of silicon, channel MSi+ --> M+ + Si is favored. Otherwise, MSi+ --> M + Si+ will be favored. A similar behavior was observed for anions, in which the dissociation channel depends on the magnitude of electron affinity.