Theoretical conformational analysis for neurotransmitters in the gas phase and in aqueous solution. Norepinephrine

The natural neurotransmitter (R)-norepinephrine takes the monocationic form in 93% abundance at the physiological tissue pH of 7.4. Ab initio and DFT/B3LYP calculations were performed for 12 protonated conformers of (R)-norepinephrine in the gas phase with geometry optimizations up to the MP2/6-311++G level, and with single-point calculations up to the QCISD(T) level at the HF/6-31G-optimized geometries. Four monohydrates were studied at the MP2/6-31G//HF/6-31G level. In the gas phase, the G1 conformer is the most stable with phenyl.NH(3)(+) gauche and HO(alc).NH(3)(+) gauche arrangements. A strained intramolecular hydrogen bond was found for conformers (G1 and T) with close NH(3)(+) and OH groups. Upon rotation of the NH(3)(+) group as a whole unit about the C(beta)-C(alpha) axis, a 3-fold potential was calculated with free energies for barriers of 3-12 kcal/mol at the HF/6-31G level. Only small deviations were found in MP2/6-311++G single-point calculations. A 2-fold potential was calculated for the phenyl rotation with free energies of 11-13 kcal/mol for the barriers at T = 310 K and p = 1 atm. A molecular mechanics docking study of (R)-norepinephrine in a model binding pocket of the beta-adrenergic receptor shows that the ligand takes a conformation close to the T(3) arrangement. The effect of aqueous solvation was considered by the free energy perturbation method implemented in Monte Carlo simulations. There are 4-5 strongly bound water molecules in hydrogen bonds to the conformers. Although hydration stabilizes mostly the G2 form with gauche phenyl.NH(3)(+) arrangement and a water-exposed NH(3)(+) group, the conformer population becomes T > G1 > G2, in agreement with the PMR spectroscopy measurements by Solmajer et al. (Z. Naturforsch. 1983, 38c, 758). Solvent effects reduce the free energies for barriers to 3-6 and 9-12 kcal/mol for rotations about the C(beta)-C(alpha) and the C(1)(ring)-C(beta) axes, respectively.     

Experimental and computational studies on zwitterionic (E)-2-(1-(2-(4-methylphenylsulfonamido)ethyliminio)ethyl) phenolate

The Schiff base compound (E)-2-(1-(2-(4-methylphenylsulfonamido)ethyliminio)ethyl) phenolate has been synthesised and characterized by IR, UV–Vis, and X-ray single-crystal determination. Ab initio calculations have been carried out for the title compound using the density functional theory (DFT) and Hartree–Fock (HF) methods at 6-31G(d) basis set. The calculated results show that the DFT/B3LYP and HF can well reproduce the structure of the title compound. Using the TD-DFT and TD-HF methods, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and the experimental ones is determined. Molecular orbital coefficient analyses reveal that the electronic transitions are mainly assigned to n → π* and π → π* electronic transitions. To investigate the tautomeric stability, optimization calculations at B3LYP/6-31G(d) level were performed for the NH and OH forms of the title compound. Calculated results reveal that the OH form is more stable than NH form. In addition, molecular electrostatic potential and NBO analysis of the title compound were performed at B3LYP/6-31G(d) level of theory.     

Molecular structures and vibrations of m-methylaniline in the S0 and S1 states studied by laser induced fluorescence spectroscopy and ab initio calculations

The UV fluorescence excitation and dispersed fluorescence spectra of a jet-cooled m-methylaniline have been obtained for the S1<--S0 transition, in which some of the bands have been observed for the first time. The main spectral bands have been assigned by comparison with those of other relevant substituted benzenes. It was found that the spectra exhibit an important feature which is the internal rotation of the methyl group in the electronic ground and excited states. Ab initio calculations at MP2/6-31G* and CIS/6-31G* show that the optimized structure of m-methylaniline in the ground state is not planar with the amino group having sp3 hybridation-like character due to the existence of lone-paired electrons on the nitrogen atom. Upon electronic excitation, the C-N bond exhibits a partial double bond character, indicating an enhanced interaction between the ring and the NH2 group as in the case of aniline.     

Vibrational dynamics of 9-fluorenemethanol using infrared-ultraviolet double-resonance spectroscopy

Vibrational spectroscopy of jet-cooled 9-fluorenemethanol and its clusters 9-fluorenemethanol-H2O, 9-fluorenemethanol-CH3OH, 9-fluorenemethanol-C2H5OH, and 9-fluorenemethanol-C3H7OH has been carried out using an IR-UV double-resonance method. The spectrum of the OH stretching vibration, v(OH), has been measured for the 9-fluorenemethanol monomer and for each of the clusters. Two conformers of 9-fluorenemethanol, symmetric (sym) and unsymmetric (unsym), have been identified using a combination of spectroscopy and quantum chemical calculations with B3LYP and HF methods using the 6-31G(d) basis set. Vibrational dynamics resulting from IR excitation has also been studied using the S0-S1 transition probed by a nanosecond-time-delayed UV laser. The data suggest that isomerization occurs as a result of the IR excitation, but the breadth of the probe spectra makes an unequivocal conclusion difficult. The effect of hydrogen bonding on the v(OH) of 9-fluorenemethanol has also been studied in clusters with water, methanol, ethanol, and propanol by measuring the IR spectra. Cluster dissociation dynamics have also been studied following IR excitation. It is observed that upon excitation of the cluster of a particular conformation the monomer product is generally produced in both conformer forms. Energetic considerations indicate that isomerization occurs before dissociation.     

Conformation of L-tyrosine studied by fluorescence-detected UV-UV and IR-UV double-resonance spectroscopy

The laser-induced fluorescence spectrum of jet-cooled L-tyrosine exhibits more than 20 vibronic bands in the 35450-35750 cm(-1) region. We attribute these bands to eight conformers by using results of UV-UV hole-burning spectroscopy. These isomers are classified into four groups; each group consists of two rotational isomers that have a similar side-chain conformation but different orientations of the phenolic OH. The splitting of band origins of rotational isomers is 31, 21, 5, and 0 cm(-1) for these groups. IR-UV spectra suggest that conformers belonging to two of the four groups have an intramolecular OH...N hydrogen bond between the COOH and NH2 groups. By comparing experimental and theoretical results of L-tyrosine with those of L-phenylalanine, we propose probable conformers of L-tyrosine.     

Modeling the H bond donor strength of ?OH, ?NH,and ?CH sites by local molecular parameters

A quantum chemical model is introduced to predict the H‐bond donor strength of monofunctional organic compounds from their ground‐state electronic properties. The model covers ? OH, ? NH, and ? CH as H‐bond donor sites and was calibrated with experimental values for the Abraham H‐bond donor strength parameter A using the ab initio and density functional theory levels HF/6‐31G** and B3LYP/6‐31G**. Starting with the Morokuma analysis of hydrogen bonding, the electrostatic (ES), polarizability (PL), and charge transfer (CT) components were quantified employing local molecular parameters. With hydrogen net atomic charges calculated from both natural population analysis and the ES potential scheme, the ES term turned out to provide only marginal contributions to the Abraham parameter A, except for weak hydrogen bonds associated with acidic ? CH sites. Accordingly, A is governed by PL and CT contributions. The PL component was characterized through a new measure of the local molecular hardness at hydrogen, η(H), which in turn was quantified through empirically defined site‐specific effective donor and acceptor energies, EE_occ and EE_vac. The latter parameter was also used to address the CT contribution to A. With an initial training set of 77 compounds, HF/6‐31G** yielded a squared correlation coefficient, r², of 0.91. Essentially identical statistics were achieved for a separate test set of 429 compounds and for the recalibrated model when using all 506 compounds. B3LYP/6‐31G** yielded slightly inferior statistics. The discussion includes subset statistics for compounds containing ? OH, ? NH, and active ? CH sites and a nonlinear model extension with slightly improved statistics (r² = 0.92). © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

Role of conformational isomerism in solvent-mediated charge transfer in chiral (S) 1,2,3,4-tetrahydro-3-isoquinoline methanol (THIQM): condensed-phase to jet-cooled spectroscopic studies

Intramolecular charge-transfer reaction in chiral (S) 1,2,3,4-tetrahydro-3-isoquinoline methanol (THIQM) has been investigated in the condensed phase and in jet-cooled conditions by means of laser-induced fluorescence, dispersed emission, resonance-enhanced two-photon ionization, and IR-UV double resonance experiments, as well as quantum chemical calculations. In the condensed phase, THIQM only shows local emission in nonpolar and protic solvents and dual emission in aprotic polar solvents, where the solvent-polarity dependent Stokes shifted emission is ascribed to a state involving charge transfer from the nitrogen lone pair to the benzene π-cloud. Ab initio calculations reveal two low-energy conformers, which are observed in jet-cooled conditions. In the most stable conformer, THIQM(I), the CH(2)OH substituent acts as a hydrogen bond donor to the nitrogen lone pair in the equatorial position, while the second most stable conformer, THIQM(II), corresponds to the opposite NH···O hydrogen bond, with the nitrogen lone pair in the axial position. The two low-energy jet-cooled conformers of THIQM evidenced from the laser-induced fluorescence and dispersed emission spectra only show structured local emission. Complexes with usual solvents reproduce the condensed phase properties. The jet-cooled complex with aprotic polar solvent acetonitrile shows both local emission and charge transfer emission as observed in solution. The jet-cooled hydrate mainly shows local emission due to the unavailability of the nitrogen lone pair through intermolecular hydrogen bonding.     

Structure of hydrated clusters of dibenzo-18-crown-6-ether in a supersonic jet--encapsulation of water molecules in the crown cavity

The structure of dibenzo-18-crown-6-ether (DB18C6) and its hydrated clusters has been investigated in a supersonic jet. Two conformers of bare DB18C6 and six hydrated clusters (DB18C6-(H(2)O)(n)) were identified by laser-induced fluorescence, fluorescence-detected UV-UV hole-burning and IR-UV double-resonance spectroscopy. The IR-UV double resonance spectra were compared with the IR spectra obtained by quantum chemical calculations at the B3LYP/6-31+G* level. The two conformers of bare DB18C6 are assigned to "boat" and "chair I" forms, respectively, among which the boat form is dominant. All the six DB18C6-(H(2)O)(n) clusters with n = 1-4 have a boat conformation in the DB18C6 part. The water molecules form a variety of hydration networks in the boat-DB18C6 cavity. In DB18C6-(H(2)O)(1), a water molecule forms the bidentate hydrogen bond with the O atoms adjacent to the benzene rings. In this cluster, the water molecule is preferentially hydrogen bonded from the bottom of boat-DB18C6. In the larger clusters, the hydration networks are developed on the basis of the DB18C6-(H(2)O)(1) cluster.     

All-trans- and t,T,t,C,t,T,t-deca-1,3,5,7,9-Pentaenes: Ab Initio Structures,Vibrational Analyses,and Some Regularities in the Series of Related Molecules

Total geometry optimization and calculation of the force constants for all-transand t,T,t,C,t,T,tdeca-1,3,5,7,9-pentaene were carried out at the ab initio, HF/6-31G level. The HF/6-31G//HF/ 6-31G force fields were modified using empirical scale factors transferred from trans-buta-1,3-diene augmented by an additional scale factor for the central formal carbon-carbon double bond coordinates (determined previously for all-trans-hexa-1,3,5-triene). The total number of scale factors was seven. The vibrational problems for both decapentaenes were solved using the respective scaled HF/6-31G//HF/6-31G force field. Infrared intensities and Raman activities were calculated from the unscaled HF/6-31G//HF/6-31G force fields. Complete assignment of all the fundamental vibrational frequencies is given. Geometrical parameters, vibrational frequencies and force constants are compared with the corresponding values of buta-1,3-diene, hexa-1,3,5-triene and octa-1,3,5,7-tetraene. Regularities in the properties of this molecular series are discussed. Special attention is given to the possibility of using the vibrational spectra for detection of distortions from the regular trans structure of these oligoenes.     

Endo-exo and facial stereoselectivity in the Diels-Alder reactions of 3-substituted cyclopropenes with butadiene

A computational examination of the four modes of addition in the Diels-Alder reactions of 3-substituted cyclopropene derivatives (substituents: BH(2), CH(3), SiH(3), NH(2), PH(2), OH, SH, F, and Cl) with butadiene have been carried out at the B3LYP/6-31++G(d)//HF/6-31++G(d) level. The degree of stabilization of these derivatives at the ground state correlates with the electronegativity of the substituent. This attenuation of reactivity and differences in steric interactions are the only factors needed to explain both the high facial selectivity and the differences in the endo-exo selectivity seen in these reactions. Furthermore, evidence is presented that indicates that stabilization by an interaction involving the syn C-3 hydrogen of cyclopropene and butadiene is small or irrelevant in controlling the endo-exo selectivity of the Diels-Alder reaction.     

Laser induced fluorescence and resonant two-photon ionization spectroscopy of jet-cooled 1-hydroxy-9,10-anthraquinone

We carried out laser induced fluorescence and resonance enhanced two-color two-photon ionization spectroscopy of jet-cooled 1-hydroxy-9,10-anthraquinone (1-HAQ). The 0-0 band transition to the lowest electronically excited state was found to be at 461.98 nm (21,646 cm(-1)). A well-resolved vibronic structure was observed up to 1100 cm(-1) above the 0-0 band, followed by a rather broad absorption band in the higher frequency region. Dispersed fluorescence spectra were also obtained. Single vibronic level emissions from the 0-0 band showed Stokes-shifted emission spectra. The peak at 2940 cm(-1) to the red of the origin in the emission spectra was assigned as the OH stretching vibration in the ground state, whose combination bands with the C=O bending and stretching vibrations were also seen in the emission spectra. In contrast to the excitation spectrum, no significant vibronic activity was found for low frequency fundamental vibrations of the ground state in the emission spectrum. The spectral features of the fluorescence excitation and emission spectra indicate that a significant change takes place in the intramolecular hydrogen bonding structure upon transition to the excited state, such as often seen in the excited state proton (or hydrogen) transfer. We suggest that the electronically excited state of interest has a double minimum potential of the 9,10-quinone and the 1,10-quinone forms, the latter of which, the proton-transferred form of 1-HAQ, is lower in energy. On the other hand, ab initio calculations at the B3LYP/6-31G(d,p) level predicted that the electronic ground state has a single minimum potential distorted along the reaction coordinate of tautomerization. The 9,10-quinone form of 1-HAQ is the lowest energy structure in the ground state, with the 1,10-quinone form lying approximately 5000 cm(-1) above it. The intramolecular hydrogen bond of the 9,10-quinone was found to be unusually strong, with an estimated bond energy of approximately 13 kcal/mol (approximately 4500 cm(-1)), probably due to the resonance-assisted nature of the hydrogen bonding involved.     

六氢吡啶和氨形成的氢键团簇C5H10NH(NH3)n(n=1～3)结构的从头算研究

在RHF/6-31G(d)水平下,对C5H10NH(NH3)n(n=1～3)氢键团簇的平衡构型进行了从头算研究,优化得到各种可能的平衡构型.C5H10NH(NH3)为线型氢键结构,而C5H10NH(NH3)2为三元环结构,C5H10NH(NH3)3为四元环结构.在MP2/6-31G(d)//B3LYP/6-31G(d)水平下,对最稳定构型C5H10NH(NH3)n(Ⅰ)(n=1～3)的分子轨道进行布居分析,并且对相应的占据轨道进行指认.C5H10NH(NH3)n(Ⅰ)(n=1～3)垂直电离势的计算结果表明,形成氢键团簇后,分子的垂直电离势降低.     

A reinvestigation of the molecular structures, vibrations and rotation of methyl group in o-methylaniline in S0 and S1 states studied by laser induced fluorescence spectroscopy and ab initio calculations

The UV fluorescence excitation and dispersed fluorescence spectra of a jet-cooled o-methylaniline have been obtained for the S1 <-- S0 transition, in which some of the bands have been observed and assigned for the first time. The origin of the electronic transition appears at 34,328.4 cm(-1). It was found that the spectra exhibit an important feature corresponding to the internal rotation of the methyl group in the electronic ground and excited states. Ab initio calculations at MP2/6-31 + G* and CIS/6-31 + G* show that the optimised structure of o-methylaniline in the ground state is not planar with the amino group having sp3 hybridation-like character due to the existence of lone paired electrons on the N atom. Upon electronic excitation, the C-N bond exhibits a partial double character, as in the case of other aniline derivatives.     

Molecular Conformation of 2,2'-Dinitrodiphenylamine According to Dielectric Studies and Ab Initio Quantum Chemical Calculations

According to the results of ab initio calculations employing the HF/6-31G* approach, the isolated 2,2'-dinitrodiphenylamine molecule exists as an sc, sc conformer stabilized by a symmetric intramolecular bifurcated (three-center) hydrogen bond. In protophilic solvents (1,4-dioxane), the conformational equilibrium is also shifted in the direction of this rotational isomer.     

氟丙烯在高温下的热稳定性

用单脉冲激波管研究了全氟丙烯C3F6的分解。使用H2作为清扫剂。产物包括 CH4、 C2F4、 CF3H和C2F3H,作为对断键反应过程的指示。C3F6的断键反应为 C3F6  CF3+C2F3 （1） 得到其速率常数表达式为 k（C3F6  CF3+C2F3)=10(17.4±0.2)exp-(355300±8360)/(RT) s-1 温度范围为1090 K相似文献   

氨和甲醇团簇中的质子转移反应

应用激光多光子电离质谱和分子束技术研究了氨和甲醇二元团簇,实验观测到两个系列质子化的团簇离子: (CH3OH)nH+和(CH3OH)nNH4+(1≤n≤14 ),其产生是经过二元团簇内的质子转移反应。同时也研究了氘代甲醇CH3OD和氨混合团簇,结果表明OD原子团中的D转移概率比CH3原子团中的质子转移概率大几倍。在HF/STO-3G和MP2/6-31G*　*水平上对氨和甲醇二元团簇进行了计算,结果表明与CH3相比OH中的质子转移更加容易,因为CH3中的质子转移过程要克服高度约120 kJ/mol的能垒。     

Theoretical estimates of the IR spectrum of water intercalated into kaolinite

Calculations at AM1, PM3, and HF/6‐31G levels of part of the IR spectrum of the water–kaolinite intercalated system based on a 96‐atom cluster of kaolinite with one water molecule are reported. Only the water molecule conformation is optimized. Frequencies and intensities for just the water vibrations and stretchings of four cluster hydroxyls were calculated through partial Hessian matrices and polar tensors obtained by numerical differentiation of energy gradients and dipole moment. The water molecule was found to attach to the cluster mainly through a double hydrogen bond to the siloxane inner surface, partially entering the siloxane ring hexagonal hole. Though the theoretical results predict that the water OH stretching frequencies decrease from the gas‐phase state to the intercalated state, they are still higher than expected with respect to the observed spectrum. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Crystal Structure and Quantum Chemical Ab Initio Calculations of Ibotenic Acid,an Excitatory Amino Acid Receptor Agonist

Ibotenic acid, a constituent of Amanita muscaria, is a potent NMDA receptor agonist. The structure of the ibotenic acid zwitterion monohydrate in the crystalline state has been determined by X-ray crystallography. The crystal structure has two ibotenic acid monohydrate formula units in the asymmetric unit and features an extensive hydrogen bond network. The ibotenic acid zwitter-ions in the crystalline state are compared to the in vacuo structure calculated by quantum chemical ab initio calculations at the HF/6-31+G* level and the effects of the hydrogen bond network on the structures in the solid state are discussed. The calculated potential energy curve with respect to side-chain orientation displays a single energy minimum. The conformations corresponding to the solid-state conformations are calculated to be ca. 2 kcal/mol higher in energy than the minimum-energy conformation in vacuo.     

Ab initio study of the conformational equilibrium of ethylene glycol

Summary The conformational equilibrium of ethylene glycol (CH₂OHCH₂OH) has been examined by performing geometry optimizations at the 6-31G*, MP2/6-31G* and 6-31G** levels. Final energies have been calculated at the MP3 level with the optimized geometries. The two most stable conformers are atGg andgGg but it is verified that the inclusion of electronic correlations reduces their energy difference of 0.6 kcal/mol at the HF level to less than 0.2 kcal/mol. The possible coexistence of the two most stable conformers is in agreement with some previous studies of Frei et al. For thetXg conformer a detailed analysis of the intramolecular potential as a function of rotation around the C-C bond is also reported.     

分子CH_3NH=B:的结构及重排反应的理论研究

采用量子化学中的从头计算方法, 在MP2/6-31G(d,p)水平上研究了不饱和硼烯CH3NH=B:的结构及重排反应机理。结果表明, CH3NH=B:的单线态结构比三线态结构稳定, 该分子的基态是单线态。分子CH3NH=B:可以发生3种不同的重排反应。本文找到了这3种重排反应的过渡态, 并详细计算了不饱和硼烯CH3NH=B:重排反应的动力学函数, 据此讨论了不饱和硼烯CH3NH=B:的稳定性问题。