Intramolecular interactions of L‐phenylalanine: Valence ionization spectra and orbital momentum distributions of its fragment molecules

Intramolecular interactions between fragments of L ‐phenylalanine, i.e., phenyl and alaninyl, have been investigated using dual space analysis (DSA) quantum mechanically. Valence space photoelectron spectra (PES), orbital energy topology and correlation diagram, as well as orbital momentum distributions (MDs) of L ‐phenylalanine, benzene and L ‐alanine are studied using density functional theory methods. While fully resolved experimental PES of L ‐phenylalanine is not yet available, our simulated PES reproduces major features of the experimental measurement. For benzene, the simulated orbital MDs for 1e_1g and 1a_2u orbitals also agree well with those measured using electron momentum spectra. Our theoretical models are then applied to reveal intramolecular interactions of the species on an orbital base, using DSA. Valence orbitals of L ‐phenylalanine can be essentially deduced into contributions from its fragments such as phenyl and alaninyl as well as their interactions. The fragment orbitals inherit properties of their parent species in energy and shape (ie., MDs). Phenylalanine orbitals show strong bonding in the energy range of 14‐20 eV, rather than outside of this region. This study presents a competent orbital based fragments‐in‐molecules picture in the valence space, which supports the fragment molecular orbital picture and building block principle in valence space. The optimized structures of the molecules are represented using the recently developed interactive 3D‐PDF technique. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Bond types of molecular orbitals and the photoelectron spectrum

The vibrational structures of the photoelectron spectra for diatomic molecules can be accounted for in terms of the slope of the orbital energy curve in the conventional correlation diagram with respect to internuclear distance. The vibrational structures of the photoelectron spectra for simple polyatomic molecules HCN, C₂H₂, and AH₂ type of hydrides can also be accounted for in terms of the slopes of the orbital energy curves in the correlation diagrams with respect to angles, as well as distances. Among all correlation diagrams, the slopes in the distance correlation diagram are related to the criterion for bond type—the positive for “bonding,” the negative for “antibonding,” while slopes with small magnitudes for “nonbonding.” The Fock matrix elements within the bond orbital basis provide heuristic and systematic rationalization of the slopes for the orbital energy curves. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 53–65, 2001     

Theoretical Study on the Hydrogen Bonding Interactions in Complexes of 5‐Hydroxytryptamine with Water

The energies, geometries and harmonic vibrational frequencies of 1:1 5‐hydroxytryptamine‐water (5‐HT‐H₂O) complexes are studied at the MP2/6‐311++G(d,p) level. Natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM) analyses and the localized molecular orbital energy decomposition analysis (LMO‐EDA) were performed to explore the nature of the hydrogen‐bonding interactions in these complexes. Various types of hydrogen bonds (H‐bonds) are formed in these 5‐HT‐H₂O complexes. The intermolecular C4H5^5‐HT···O^w H‐bond in HTW3 is strengthened due to the cooperativity, whereas no such cooperativity is found in the other 5‐HT‐H₂O complexes. H‐bond in which nitrogen atom of amino in 5‐HT acted as proton donors was stronger than other H‐bonds. Our researches show that the hydrogen bonding interaction plays a vital role on the relative stabilities of 5‐HT‐H₂O complexes.     

Structures,vibrational frequencies,topologies, and energies of hydrogen bonds in cysteine‐formaldehyde complexes

The hydrogen bonding interactions between cysteine (Cys) and formaldehyde (FA) were studied with density functional theory regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules and natural bond orbital analyses were employed to elucidate the interaction characteristics in the Cys‐FA complexes. The intramolecular hydrogen bonds (H‐bonds) formed between the hydroxyl and the N atom of cysteine moiety in some Cys‐FA complexes were strengthened because of the cooperativity. Most of intermolecular H‐bonds involve the O atom of cysteine/FA moiety as proton acceptors, while the strongest H‐bond involves the O atom of FA moiety as proton acceptor, which indicates that FA would rather accept proton than providing one. The H‐bonds formed between the CH group of FA and the S atom of cysteine in some complexes are so weak that no hydrogen bonding interactions exist among them. In most of complexes, the orbital interaction of H‐bond is predominant during the formation of complex. The electron density (ρ_b) and its Laplace (?²ρ_b) at the bond critical point significantly correlate with the H‐bond parameter δR, while a linearly relationship between the second‐perturbation energy E(2) and ρ_b has been found as well. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

氢卟啉和镁卟啉分子溶剂效应的理论研究

采用溶剂场极化连续模型在密度泛函B3LYP/6-31G (D)水平上研究了氢卟啉和镁卟啉分子在四氢呋喃(THF)、二甲基亚砜(DMSO)、二氯甲烷(CH2Cl2)、氯仿(CHCl3)这四种不同极性的溶剂环境中的几何结构和分子轨道能级, 从而研究了溶剂效应引起的分子几何构型和轨道能级的变化. 然后采用上述溶剂环境下优化的几何结构在含时密度泛函水平上计算了它们的激发能、吸收波长、跃迁组成和振荡强度. 理论计算结果表明, 对比真空条件下的氢卟啉和镁卟啉分子的几何结构, 溶剂场中两种卟啉分子的几何结构都发生了微弱的变化, 这种变化随溶剂介电常数的增大而有所增强. 计算结果表明溶剂环境中氢卟啉和镁卟啉分子的电子吸收光谱发生了普遍的红移, 结合分子轨道理论对这种变化给出了可能的解释. 在此基础上, 对这种包含溶剂效应的理论分析方法用于检验卟啉类化合物作为染料敏化太阳能电池光敏剂的可行性作了进一步的探讨.     

Structures,energetics, and isomerism of [Be,C,O,S]: Stability of triply bonded sulfur

Multiply bonded sulfur has continued to attract attention both experimentally and theoretically. Triply sulfur‐bonded compounds are still rare, due to either the lack of suitable generation precursors or the conversion instability toward doubly sulfur‐bonded structures. A detailed computational study was performed on the structures and stability of various [Be,C,O,S] isomers at the coupled cluster singles doubles (triple excitations) (CCSD(T))/aug‐cc‐pVTZ//B3LYP/6‐311+G(d)+ZPVE level to predict intrinsically stable isomers with triply bonded sulfur. The molecular orbital, bond distance, and harmonic vibrational frequency analysis were carried out at aug‐cc‐pVTZ‐B3LYP, M06‐2X, and CCSD(T) levels to investigate the bonding nature of linear structures. It was shown that two low‐lying isomers are linear SBeCO 01 (0.0 kcal/mol) and SBeOC 02 (15.7 kcal/mol), both of which possess the SBe triple bonding. The Lewis acid–base association of SBe + CO can barrierlessly form 01 and 02, with the former more abundant, while the insertion reaction of SCO + Be might generate more 02 than 01 via photochemical processes. By contrast, formation of the SC‐bearing isomer SCBeO 04 (39.4 kcal/mol) seems unlikely due to its higher energy and less kinetic competition than that of 01 and 02, via either simple association or insertion reactions. The new stable isomers SBeCO 01 and SBeOC 02 add to the number of SBe triply bonded species. Their unique structures and varied branching ratios under association and insertion processes deserve future experimental study. © 2013 Wiley Periodicals, Inc.     

Ab initio studies of the conformers and conformational distribution of gas‐phase N,N‐dimethylaminopropanol

Systematic and extensive conformational search has been performed to characterize the gas‐phase N,N‐dimethylaminopropanol structures. A total of 91 unique trail structures were generated by allowing for all the single‐bond rotamers. All the trial structures were initially optimized at the AM1 level, and the resulting structures were optimized at the B3LYP/6‐311G* level of theory and then subjected to further optimization at the B3LYP/6‐311++G**. A total of 36 conformers are found and their zero‐point vibrational enegies, rotational constants, and dipole moments are determined. Vertical ionization energies of 11 low‐lying conformers predicted with the electron propagator theory are in good agreement with the experimental data. The two most stable conformers display intramolecular H bonds (HBs): OH···N. These HBs influence on the molecular electronic structures is exhibited by natural bond orbital analyses. Combined with statistical mechanics principles, conformational distributions at various temperatures are computed and the temperature dependence of photoelectron spectra is interpreted. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Conformational Distributions of N‐Acetyl‐L‐cysteine in Aqueous Solutions: A Combined Implicit and Explicit Solvation Treatment of VA and VCD Spectra

The conformational distributions of N‐acetyl‐L ‐cysteine (NALC) in aqueous solutions at several representative pH values are investigated using vibrational absorption (VA), UV/Vis, and vibrational circular dichroism (VCD) spectroscopy, together with DFT and molecular dynamics (MD) simulations. The experimental VA and UV/Vis spectra of NALC in water are obtained under strongly acid, neutral, and strongly basic conditions, as well as the VCD spectrum at pH 7 in D₂O. Extensive searches are carried out to locate the most stable conformers of the protonated, neutral, deprotonated, and doubly deprotonated NALC species at the B3LYP/6‐311++G(d,p) level. The inclusion of the polarizable continuum model (PCM) modifies the geometries and the relative stabilities of the conformers noticeably. The simulated PCM VA spectra show significantly better agreement with the experimental data than the gas‐phase ones, thus allowing assignment of the conformational distributions and dominant species under each experimental condition. To further properly account for the discrepancies noted between the experimental and simulated VCD spectra, PCM and the explicit solvent model are utilized. MD simulations are used to aid the modelling of the NALC–(water)_N clusters. The geometry optimization, harmonic frequency calculations, and VA and VCD intensities are computed for the NALC–(water)_3,4 clusters at the B3LYP/6‐311++G(d,p) level without and with the PCM. The inclusion of both explicit and implicit solvation models at the same time provides a decisively better agreement between theory and experiment and therefore conclusive information about the conformational distributions of NALC in water and hydrogen‐bonding interactions between NALC and water molecules.     

From Amino Acids to High‐Energy Dense Oxidizers: Polynitro Materials Derived from β‐Alanine and L‐Aspartic Acid

New oxygen‐rich compounds starting from the amino acids β‐alanine and L ‐aspartic acid were synthesized and comprehensively analyzed including multinuclear NMR spectroscopy and vibrational spectroscopy. Thermal stabilities were measured and the behavior towards external stimuli like friction or impact were determined. Detonation and combustion parameters were predicted by using the EXPLO5 V6.02 code and were compared with common explosives. In addition, crystal structures were obtained for two compounds.     

A detailed theoretical study on the excited‐state hydrogen‐bonding dynamics and the proton transfer mechanism for a novel white‐light fluorophore

In this work, density functional theory (DFT) and time‐dependent DFT (TDDFT) methods were used to investigate the excited‐state dynamics of the excited‐state hydrogen‐bonding variations and proton transfer mechanism for a novel white‐light fluorophore 2‐(4‐[dimethylamino]phenyl)‐7‐hyroxy‐6‐(3‐phenylpropanoyl)‐4H‐chromen‐4‐one ( 1 ). The methods we adopted could successfully reproduce the experimental electronic spectra, which shows the appropriateness of the theoretical level in this work. Using molecular electrostatic potential (MEP) as well as the reduced density gradient (RDG) versus the product of the sign of the second largest eigenvalue of the electron density Hessian matrix and electron density (sign[λ₂]ρ), we demonstrate that an intramolecular hydrogen bond O1–H2···O3 should be formed spontaneously in the S₀ state. By analyzing the chemical structures, infrared vibrational spectra, and hydrogen‐bonding energies, we confirm that O1–H2·O3 should be strengthened in the S₁ state, which reveals the possibility of an excited‐state intramolecular proton transfer (ESIPT) process. On investigating the excitation process, we find the S₀ → S₁ transition corresponding to the charge transfer, which provides the driving force for ESIPT. By constructing the potential energy curves, we show that the ESIPT reaction results in a dynamic equilibrium in the S₁ state between the forward and backward processes, which facilitates the emission of white light.     

QR‐SCMEH‐MO calculations on the complex [Pt (SnCl3)5]3−: Electronic structure,UV–visible spectrum,magnetic properties,and bond energy

A molecular orbital study via the QR‐SCMEH‐MO (quasi‐relativistic self consistent modified extended H?ckel molecular orbital) method has been carried out on the unusual Pt 5‐ coordinated complex Pt (SnCl₃). The computed UV–Visible spectral data and NMR parameters are found to be in good agreement with the reported experimental values. In addition, the magnetic susceptibility and Pt? Sn bond energy have been calculated, although there are no reported experimental data with which to compare these results. Pt? Sn bond energies of other Pt‐SnX₃ (X = Cl, Br) systems and are compared with proposed bond energy trends based on NMR and observed bond distances. © 2012 Wiley Periodicals, Inc.     

Molecular structure and vibrational assignment of α‐chloro acetylacetone: A density functional theory study

The intramolecular hydrogen bond, molecular structure, and vibrational frequencies of α‐chloro acetylacetone have been investigated. Fourier transform infrared and Fourier transform Raman spectra of this compound and its deuterated analogue were recorded in the regions 400–4,000 cm^?1 and 50–4,000 cm^?1, respectively. Rigorous normal coordinate analysis has been performed at the B3LYP/6‐311++G** level of theory for purposes of comparison. The complete vibrational assignment for TFAA has been made on the basis of the calculated potential energy distribution. We also applied the atoms in molecules theory and natural bond orbital method for the analysis of the hydrogen bond in α‐Chloro acetylacetone and acetylacetone. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Theoretical study of the red‐ and blue‐shifted hydrogen bonds of nitroxyl and acetylene dimers

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the C? H…O red‐shifted and N? H…π blue‐shifted hydrogen bonds in HNO? C₂H₂ dimers. The geometric structures, vibrational frequencies and interaction energies were calculated by both standard and counterpoise (CP)‐corrected methods. In addition, the G3B3 method was employed to calculate the interaction energies. The topological and natural bond orbital (NBO) analysis were investigated the origin of N? H…π blue‐shifted hydrogen bond. From the NBO analysis, the electron density decrease in the σ* (N? H) is due to the significant electron density redistribution effect. The blue shifts of the N? H stretching frequency are attributed to a cooperative effect between the rehybridization and electron density redistribution. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Multi spectroscopic and computational investigations on the electronic structure of oxyclozanide

The present work contributes to a combined theoretical and experimental investigation on oxyclozanide. The experimental vibrational spectra were characterized by Fourier transform infrared (4000-400 cm^?1), Fourier transform Raman (4000-400 cm^?1), ¹H and ¹³C NMR were recorded in Deuterated methanol, UV–Vis (200–400 nm) techniques and theoretical optimized molecular geometry, harmonic vibrational spectra, magnetic spectra, and electronic spectra was calculated by Density Functional Theory (DFT) employed with B3LYP/6-311++G(d,p) basis set and compared with experimental data. The highest occupied molecular orbital - lowest unoccupied molecular orbital (HOMO-LUMO) energy was also calculated for the titled compound. The intermolecular interactions have been addressed through Hirshfeld surface analysis. In addition, Natural bond orbital (NBO) analyses of the title compound were performed to evaluate the suitable reactivity site and chemical stabilization behavior, Mulliken atomic charge distribution, and molecular electrostatic potential energy surfaces, were calculated to get a better insight into the structure of oxyclozanide. The experimental and theoretical findings suggest an excellent correlation to confirm the structure of oxyclozanide.     

New hydrophobic L‐amino acid salts: maleates of L‐leucine,L‐isoleucine and L‐norvaline

Crystals of maleates of three amino acids with hydrophobic side chains [L‐leucenium hydrogen maleate, C₆H₁₄NO₂⁺·C₄H₃O₄⁻, (I), L‐isoleucenium hydrogen maleate hemihydrate, C₆H₁₄NO₂⁺·C₄H₃O₄⁻·0.5H₂O, (II), and L‐norvalinium hydrogen maleate–L‐norvaline (1/1), C₅H₁₁NO₂⁺·C₄H₃O₄⁻·C₅H₁₂NO₂, (III)], were obtained. The new structures contain C₂²(12) chains, or variants thereof, that are a common feature in the crystal structures of amino acid maleates. The L‐leucenium salt is remarkable due to a large number of symmetrically non‐equivalent units (Z′ = 3). The L‐isoleucenium salt is a hydrate despite the fact that L‐isoleucine is a nonpolar hydrophobic amino acid (previously known amino acid maleates formed hydrates only with lysine and histidine, which are polar and hydrophilic). The L‐norvalinium salt provides the first example where the dimeric cation L‐Nva...L‐NvaH⁺ was observed. All three compounds have layered noncentrosymmetric structures. Preliminary tests have shown the presence of the second harmonic generation (SGH) effect for all three compounds.     

Source of Cooperativity in Halogen‐Bonded Haloamine Tetramers

Inspired by the isostructural motif in α‐bromoacetophenone oxime crystals, we investigated halogen–halogen bonding in haloamine quartets. Our Kohn–Sham molecular orbital and energy decomposition analysis reveal a synergy that can be traced to a charge‐transfer interaction in the halogen‐bonded tetramers. The halogen lone‐pair orbital on one monomer donates electrons into the unoccupied σ*_N?X orbital on the perpendicular N?X bond of the neighboring monomer. This interaction has local σ symmetry. Interestingly, we discovered a second, somewhat weaker donor–acceptor interaction of local π symmetry, which partially counteracts the aforementioned regular σ‐symmetric halogen‐bonding orbital interaction. The halogen–halogen interaction in haloamines is the first known example of a halogen bond in which back donation takes place. We also find that this cooperativity in halogen bonds results from the reduction of the donor–acceptor orbital‐energy gap that occurs every time a monomer is added to the aggregate.     

Theoretical study of energies,structures, and vibrational spectra of the carbonic acid–hydroperoxy radical complexes

In this work, we present the results for the first time of our study on hydrogen‐bonded H₂CO₃–HO₂ complexes (structures 1, 2) by means of ab initio molecular orbital theory. These complexes are important intermediates in the reaction of the hydroperoxy radical and cabonic acid. We calculated that these structures are a six‐membered ring. We found that the binding energy of two complexes are 5.8 and 9.3 kcal/mol using the CCSD(T) method. We also calculated the vibrational and rotational frequencies for these complexes. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

ONIOM and FMO‐EDA study of metabotropic glutamate receptor 1: Quantum insights into the allosteric binding site

The crystal structure of metabotropic glutamate receptor 1 (mGluR1) complexed with 4‐fluoro‐N‐(4‐(6‐(isopropylamino)pyrimidin‐4‐yl)thiazol‐2‐yl)‐N‐methylbenzamide (FITM, a negative allosteric modulator) and its twelve close structural analogs with a broad spectrum of affinities (2.4 nM < IC₅₀ > 10 000 nM) were investigated using quantum mechanical methods. The our own N‐layered integrated molecular orbital and molecular mechanics (ONIOM) was used to optimize the molecular geometries of the receptor with complexed ligands, which were then used to perform the ab initio calculations using the fragment molecular orbitals method with energy decomposition analysis (FMO‐EDA). The results clearly showed that residues Q660^3.28 and/or Y805^6.55 were the anchoring points for all the studied analogs of FITM, while the H‐bond with T815^7.38 determined only the orientation of very active molecules containing an amino substituent in the pyrimidine moiety (e.g., FITM). The orientation of the other parts of ligands resulted from hydrophobic interactions mainly with L757^5.44, F801^6.51, or W798^6.48. The applied ONIOM/FMO–EDA approach facilitated the study of effects related to very small changes in the ligand structure and led to conclusions regarding the significance of individual interactions in the allosteric binding pocket of mGluR1.     

Photoelectrochemical Detection of L‐Cysteine with a Covalently Grafted ZnTAPc‐Gr‐based Probe

L‐cysteine plays a vital role in organisms, and is an important biomarker for many pathological diseases that seriously affect human health. In the study, a photoelectrochemical (PEC) probe with zinc‐tetramine phthalocyanine covalently grafted to graphene oxide (ZnTAPc‐Gr) was developed for L‐cysteine detection. Graphene oxide (GO) with carboxyl was used to immobilize zinc‐tetramine phthalocyanine (ZnTAPc) with amidogen (a graft structure formed by an amide covalent bond), which could firmly immobilize ZnTAPc, thereby improving the photoelectrochemical performance and stability. L‐cysteine molecule, an electron acceptor, was specifically recognized by the PEC probe, exhibiting a decrease in the photocurrent signal. Under the optimal experimental conditions, the fabricated PEC probe exhibited excellent performance in L‐cysteine analysis within a linear range of 0.25–113 μM and a detection limit of 11.4 nM. The PEC probe showed high sensitivity, selectivity, and stability. The method described herein provides an effective strategy for PEC probe construction for L‐cysteine detection, and can also serve as a promising PEC platform for the analyses of other small molecules.     

蒽醌及其羟基衍生物的密度泛函理论研究

运用密度泛函理论, 在B3LYP/6-31G*水平上, 对蒽醌及其羟基取代衍生物进行理论计算. 几何全优化的结果表明, 标题化合物均取平面构型, 分子内氢键对几何构型和电子结构影响很大. 基于简谐振动分析求得IR谱频率和强度, 并作了对称性分类和指认, 计算值与实验值良好相符. 运用含时密度泛函理论方法在相同水平上计算了标题物的电子吸收光谱, 发现蒽醌芳环取代衍生物的最低激发单重态均源自HOMO-LUMO(π→π*)跃迁. 基于振动分析, 由统计热力学求得了标题物的热力学性质.