A quantum chemical study of an isogermacrone-type molecule

A quantum chemical study of the electronic factors affecting the photochemical behaviour of 13-nor-E,E-isogermacrone, a sesquiterpene-type ketone, has been carried out. The results indicate that the parallel endo double bond intramolecular cyclization to cyclobutanes proceeding through n, π* excited states is strongly favoured, the interaction between the crossed endo double bonds also being possible.     

Origin of tight binding of a near-perfect transition-state analogue by cytidine deaminase: implications for enzyme catalysis

Cytidine deaminase (CDA) is a zinc metalloenzyme that catalyzes the hydrolytic deamination of cytidine to uridine. Zebularine (ZEB) binds to CDA, and the binding process leads to a near-perfect transition-state analogue (TSA) inhibitor at the active site with an estimated K(i) value of 1.2 x 10(-)(12) M. The interaction of CDA with the TSA inhibitor has become a paradigm for studying the tight TSA binding by enzymes. The formation of the TSA is catalyzed by CDA by a mechanism that is similar to the formation of the tetrahedral intermediate during the CDA-catalyzed reaction (i.e., through the nucleophilic attack of a Zn-hydroxide group on C(4)). It is believed that the TSA formed at the active site is zebularine 3,4-hydrate. In this paper, it is shown from QM/MM molecular dynamics and free energy simulations that zebularine 3,4-hydrate may in fact be unstable in the enzyme and that a proton transfer from the Zn-hydroxide group to Glu-104 during the nucleophilic attack could be responsible for the very high affinity. The nucleophilic attack by the Zn-hydroxide on C(4) is found to be concerted with two proton transfers. Such concerted process allows the TSA, an alkoxide-like inhibitor, to be stabilized through a mechanism that is similar to the transition-state stabilization in the general acid-base catalysis. It is suggested that the proton transfer from the Zn-hydroxide to Glu-104, which is required to generate the general acid for protonating the leaving ammonia, may play an important role in lowering the activation barrier during the catalysis.     

Aspects of the mechanism of catalysis of glucose oxidase: A docking, molecular mechanics and quantum chemical study

The complex structure of glucose oxidase (GOX) with the substrate glucose was determined using a docking algorithm and subsequent molecular dynamics simulations. Semiempirical quantum chemical calculations were used to investigate the role of the enzyme and FAD co-enzyme in the catalytic oxidation of glucose. On the basis of a small active site model, substrate binding residues were determined and heats of formation were computed for the enzyme substrate complex and different potential products of the reductive half reaction. The influence of the protein environment on the active site model was estimated with a point charge model using a mixed QM/MM method. Solvent effects were estimated with a continuum model. Possible modes of action are presented in relation to experimental data and discussed with respect to related enzymes. The calculations indicate that the redox reaction of GOX differs from the corresponding reaction of free flavins as a consequence of the protein environment. One of the active site histidines is involved in substrate binding and stabilization of potential intermediates, whereas the second histidine is a proton acceptor. The former one, being conserved in a series of oxidoreductases, is also involved in the stabilization of a C4a-hydroperoxy dihydroflavin in the course of the oxidative half reaction.     

The water molecule arrangement over the side chain of some aliphatic amino acids: A quantum chemical and bottom-up investigation

The geometry of surrounding water molecules on the side chain of glycine, alanine, α-aminoisobutyric acid, α-aminobutyric acid, valine, and related hydrocarbons has been analyzed combining bottom-up and quantum chemical methodologies. To minimize the cavity size and to prevent water-water hydrogen bonding loss, the water molecules adopt a shape, resembling the one found in crystal structure of gas clathrate hydrates, with water molecules tangentially oriented to the surface of hydrophobic side chain. The cage is directly hydrogen bonded to the backbone's polar groups, thus hydration shells around hydrophobic and hydrophilic groups are folded together in amphiphilic molecules. The hydrophobe enclathration implies a substantial freedom degree reduction which makes it entropically disfavored. This disadvantageous entropic contribution is partially compensated by the favorable van der Waals interactions with guest in stabilizing clathrate hydrate formation. The water shell around the side chain relates intimately with the side-chain rotational isomerism. Present data are correlated with the experimental determined populations of the three rotamers, yielding promising results for both α-aminobutyric acid and valine.     

Analyzing the contribution of material science in quantum cryptography: A scientometric study

Quantum cryptography (QC) provides security to information through laws of nature, particularly quantum mechanics. The necessity of making QC a living reality has provided the impetus to advancement in material science, which led to many publications since 1996. Therefore, in this work, we analyze the articles in the Scopus database concerning the contribution of material science in the development of QC through scientometric methods. A total of 1395 articles published from 1996 to 2022 were retrieved from the Scopus database. Subsequently, these articles were analyzed to retrieve publication patterns, major collaborating nations, significant documents, recent trends, and future directions. A comprehensive introduction to QC is also included to facilitate a better grasp of this field for a wide range of readers. The findings of this study show that China is the leading nation in developing QC through material science, closely followed by the United States and India. Moreover, the study indicates significant areas of QC where extensive work is being done from the material science standpoint through keyword and significant document analysis. Hence, the outcomes of this article can be valuable for researchers, newcomers, technology managers, and policymakers interested in the future of QC.     

Sandwich compounds of second-row elements: A quantum chemical study

The structures and stabilities of a number of neutral and charged sandwich-type boron, carbon, and nitrogen compounds designed based on the cyclophane cage and obeying the “electron octet” rule were studied by the B3LYP/6−311+G** density functional method. The possibility of targeted modification of the electronic structures of such compounds by varying the basal or bridging atomic groups was investigated. Dedicated to Academician O. M. Nefedov on the occasion of his 75th birthday. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 1825–1835, November, 2006.     

Gas electron diffraction and quantum chemical study of the structure of a 2-nitrobenzenesulfonyl chloride molecule

A combined gas electron diffraction and quantum chemical (B3LYP/6-311+G**, B3LYP/cc-pVTZ, B3LYP/cc-pVTZ, midix (Cl), and MP2/cc-pVTZ) study of the structure of a 2-NO₂-C₆H₄-SO₂Cl molecule is performed. It is found experimentally that at a temperature of 345(5) K the gas phase contains two conformers of the C ₁ symmetry. Conformer I with a nearly perpendicular arrangement of the S-Cl bond with respect to the benzene ring plane (the C(NO₂)-C-S-Cl torsion angle is 84(3)°) is contained predominantly (69(12)%). In conformer II, the S-Cl bond is located near the benzene ring plane (the C(NO₂)-C-S-Cl angle is 172(3)°). The following experimental internuclear distances (Å) are obtained for conformer I: r _h1(C-H) = 1.064(15), r _h1(C-C)_av = 1.397(3), r _h1(C-S) = 1.761(6), r _h1(S-O)_av = 1.426(4), r _h1(S-Cl) = 2.043(5), r _h1(N-O)_av = 1.222(4), r _h1(C-N) = 1.485(16). In both conformers, the NO₂ group is turned by more than 30° relative to the benzene ring plane.     

Silver clusters in the cages of zeolites: A quantum chemical study

The electronic structure of zeolite A is developed in a step by step procedure from the simple O_hH₈Si₈O₁₂ molecule, to the _∞ ¹ [(-O)₂H₄[Si₈O₁₂)] chain, to the _∞ ² [(-O₄)(Si₈O₁₂)] layer, and finally to the silica zeolite A framework _∞ ³ [Si₂₄O₄₈]. It is remarkable how well the calculated band structures of both, _∞ ² [(-O)₄(Si₈O₁₂)] and _∞ ³ [Si₂₄O₄₈] correspond to the experimentally determined band structure of α-quartz with a Fermi level of -10.55 eV. The HOMO region consists in each case of nonbonding 2p-oxygen bands which in a localized language can be denoted as oxygen lone pairs ( | O<). We observe in each case the typical behaviour of an insulator with saturated valencies whose electronic structure can be described as being localized and is already present in the starting O_h-H₈Si₈O₁₂ molecule. The double-8-rings D8R of the _∞ ² [(-O)₄(Si₈O₁₂)] layer have a pore diameter of 4.1 Å, the same as the pore opening of zeolite A. It is large enough to accept up to four Ag, forming _∞ ² [(-O)₄(Si₈O₁₂)Ag_n], n = 1, 2, 3, 4, layers, suitable for modelling the electronic interactions between the zeolite cavity embedded silver clusters and between the clusters and the zeolite framework. With one Ag per D8R the band structure is simply a superposition of the 4d, 5s and 5p levels of a layer of nearly noninteracting Ag and the silicon dioxide layer. The Ag-d band lies below the oxygen lone pairs, the Ag-s band lies about 3 eV above the oxygen lone pairs, and the Ag-5p bands are in the antibonding silicon dioxide region. The first electronic transition is of oxygen lone pair to Ag-5s LMCT type. Increasing silver content results in progressive splitting of the 5σ Ag bands and shifts the first (Ag^m+ _n)? ← (| O<) charge transfer transition to lower energies. The filled Ag 4d-bands lie always significantly below the (| O<) HOCOs (highest occupied crystal orbitals) but their band width increases with increasing silver content. In all cases the zeolite environment separates the Ag clusters through antibonding Ag-(← O<) interactions so that the coupling remains weak and it makes sense to describe the Ag clusters in the D8R as quantum dots weakly interacting with each other.     

A quantum chemical study on electrophilic addition

Non-empirical SCF-MO calculations were carried out on two limiting structures of C₂H₄F⁺, corresponding to the cyclic and open valence tautomers, both of which are possible reaction intermediates of the electrophilic addition reaction of F₂ to CH₂ =CH₂. It was found that both species had thermodynamic stability, corresponding to two distinct minima on the energy surface. However, the 2-fluoroethyl carbonium ion showed a greater stability than the fluoronium ion by about 10 kcal/mole.     

Gas-phase electron diffraction and quantum chemical study of the structure of the 4-nitrobenzene sulfonyl chloride molecule

A combined gas-phase electron diffraction and quantum chemical (B3LYP/6-311+G**, B3LYP/cc-pVTZ, MP2/6-31G*, and MP2/cc-pVTZ) study of the structure of the 4-nitrobenzene sulfonyl chloride molecule is performed. It is found that at a temperature of 391(3) K only one conformer with C _s symmetry is present in the gas phase. The following experimental values of structural parameters are obtained: r _h1(C-H)_av = 1.086(6) Å, r _h1(C-C)_av = 1.395(3) Å, r _h1(C1-S) = 1.773(4) Å, r _h1(S=O) = 1.423(3) Å, r _h1(S-Cl) = 2.048(4) Å, r _h1(N-O) = 1.224(3) Å, r _h1(N-C4) = 1.477(3) Å, ∠(C1-S=O) = 109.0(4)°, ∠(Cl-S-O) = 106.7(2)°, ∠C1-S-Cl = 100.2(13)°, ∠O=S=O = 122.9(11)°, ∠O=N=O = 123.6(5)°. The C2-C1-S-Cl torsion angle that characterizes the position of the S-Cl bond relative to the benzene ring plane is 89(4)°. The NO₂ group lies in the benzene ring plane. Internal rotation barriers calculated by B3LYP/6-311+G** and MP2/6-31G* methods are: V ₁ = 4.7 kcal/mol and 5.3 kcal/mol for the sulfonyl chloride group; V ₂ = 4.9 kcal/mol and 6.0 kcal/mol for the nitro group.     

Nonadiabatic transitions in chemical reactions: A quantum mechanical study

This work presents an exact quantum mechanical treatment of a reactive three-atom collinear model system incorporating nonadiabatic couplings. It was assumed that nonadiabatic transitions are induced by the vibrational motion only. The main findings are: (i) The reaction process can create conditions in which weak nonadiabatic couplings terms ( for which the Massey parameter was round 10) may cause large probabilities (～0.5) for transitions from one electronic surface to the other. In other words, the reaction process is able in certain cases to create a near resonance situation which makes the non-adiabatic transition almost independent of the magnitude of the coupling term. For this to happen the two surfaces need not be proximate, nor need they “almost” cross along a certain line (ii) In cases where the main nonadiabatic transitions take place outside the interaction region one may, at least qualitatively, decouple the reaction process from the nonadiabatic one. Thus, under the conditions specified one may first treat the reactive system on the ground state surface without including the excited interacting surface and then treat the nonadiabatic process independently.     

A microwave and quantum chemical study of allyltrifluorosilane

The structural and conformational properties of allytrifluorsilane, H₂CCH-CH₂-SiF₃, have been explored by microwave (MW) spectroscopy and high-level ab initio and density functional theory quantum chemical calculations. The microwave spectrum was investigated in the 18-62 GHz spectral regions. The a-type R-branch transitions of one conformer were assigned for the ground as well as for 10 vibrationally excited states. The CC-C-Si chain of atoms in this rotamer takes an anti-clinal (‘skew’) conformation, with a dihedral angle calculated to be 111.6° from the syn-periplanar (0°) conformation. The question whether a CC-C-Si syn-periplanar conformer exists as a high-energy form in the gas phase remains open. In most of the quantum chemical calculations this conformation is predicted to be a transition state. However, in the most advanced calculations (B3LYP/aug-cc-pVTZ level of theory) the syn-periplanar conformer is predicted to be a stable rotamer that is calculated to be 6.5 kJ/mol higher in energy than the anti-clinal form. Since there is no indication in the MW spectrum for the presence of high-energy form(s), it is concluded that the anti-clinal conformer is at least 4 kJ/mol more stable than any other hypothetical rotamer.     

A microwave and quantum chemical study of cyclopropaneselenol

The microwave spectrum of cyclopropaneselenol, C 3H 5SeH, has been investigated in the 21.9-80 GHz frequency range. The microwave spectra of the ground vibrational state of five isotopologues of cyclopropaneselenol (C 3H 5 (82)SeH, C 3H 5 (80)SeH, C 3H 5 (78)SeH, C 3H 5 (77)SeH, and C 3H 5 (76)SeH) of one conformer, as well as the spectra of two vibrationally excited states of each of the C 3H 5 (80)SeH and C 3H 5 (78)SeH isotopologues of this rotamer, have been assigned. The H-C-Se-H chain of atoms is synclinal in this conformer, and there is no indication of further rotameric forms in the microwave spectrum. The b-type transitions of the ground vibrational state of the more abundant species C 3H 5 (80)SeH and C 3H 5 (78)SeH were split into two components, which is assumed to arise from tunneling of the proton of the selenol group between two equivalent synclinal potential wells. The tunneling frequencies were 0.693(55) MHz for C 3H 5 (80)SeH and 0.608(71) MHz for C 3H 5 (78)SeH. The microwave study has been augmented by high-level density functional and ab initio quantum chemical calculations, which indicate that the H-C-Se-H dihedral angle is approximately 75 degrees from synperiplanar (0 degrees).     

A microwave and quantum chemical study of cyclopropanethiol

The microwave spectra of cyclopropanethiol, C(3)H(5)SH, and one deuterated species C(3)H(5)SD, have been investigated in the 20 - 80 GHz frequency range. The spectra of the ground vibrational state and of three vibrationally excited states of the parent species of a conformer which has a synclinal ("gauche") arrangement for the H-C-S-H chain of atoms, was assigned. The H-C-S-H dihedral angle is 76(5)° from synperiplanar (0°). The b-type transitions of the ground and of the vibrationally excited states of the parent species were split into two components, which is assumed to arise from tunneling of the proton of the thiol group between two equivalent synclinal potential wells. No splitting was resolved in the spectrum of C(3)H(5)SD. The tunneling frequency of the ground vibrational state of C(3)H(5)SH is 1.664(22) MHz. The tunneling frequency of the first excited-state of the C-S torsion is 52.330(44) MHz, whereas this frequency is 26.43(13) and 3.286(61) MHz, respectively, for the first excited states of the two lowest bending vibrations. The dipole moment of the ground vibrational state of the parent species is μ(a) = 4.09(5), μ(b) = 2.83(11), μ(c) = 0.89(32), and μ(tot) = 5.06(16) × 10(-30) C m. The microwave study has been augmented by high-level density functional and ab initio quantum chemical calculations.     

A quantum chemical study of the decomposition of Keggin-structured heteropolyacids

Heterpolyacids (HPAs) demonstrate catalytic activity for oxidative and acid-catalyzed hydrocarbon conversion processes. Deactivation and thermal instability, however, have prevented their widespread use. Herein, ab initio density functional theory is used to study the thermal decomposition of the Keggin molecular HPA structure through the desorption of constitutional water molecules. The overall reaction energy and activation barrier are computed for the overall reaction HnXM12O40-->Hn-2XM12O39+H2O. and subsequently used to predict the effect of HPA composition on thermal stability. For example, the desorption of a constitutional water molecule is found to be increasingly endothermic in the order silicomolybdic acid (H4SiMo12O40)相似文献   

A quantum chemical study of the mechanism of manganese catalase

The catalytic mechanism of manganese catalase has been studied using the Becke's three parameter hybrid method with the Lee, Yang and Parr correlation functional. On the basis of available experimental information on the geometric and electronic structure of the active manganese dimer complex, different possibilities were investigated. The mechanism finally suggested consists of eight steps. In the first steps, the first hydrogen peroxide becomes bound and its O–O bond is activated. This occurs in a spin-forbidden process found to be common in many biological processes where the O–O bond is cleaved, and two general rules are formulated for the requirements for a low activation energy in this type of reaction. As the O–O bond is cleaved a hydroxyl radical is initially formed in the overall rate-limiting step of the catalytic cycle. This radical is then immediately and irreversibly quenched in a strongly exothermic step. In the subsequent steps, the second hydrogen peroxide becomes bound and its two O–H bonds are broken, leading to the formation of an O₂ molecule, which is released. Parallels between the reversal of the present O–O cleavage mechanism in manganese catalase and the recently suggested O–O bond formation in photosystem II are drawn. Received: 12 July 2000 / Accepted: 12 July 2000 / Published online: 21 December 2000     

Hydrolysis of tetrafluorosilane under neutral conditions: A quantum chemical study

A density functional quantum chemical study of the first step of SiF₄ hydrolysis under neutral conditions in the presence of one or two H₂O molecules was carried out. The reaction is endothermic and can follow three different pathways that involve the formation of penta-coordinated (pathway A) and hexacoordinated (pathways B and C) intermediates and transition states as the key steps. Pathway B is the most energetically favorable. All three pathways of the hydrolysis reaction lead to a product with formal retention of the configuration of substituents at the silicon atom. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 749–753, May, 2006.     

The Stevens rearrangement of methylenedimethyloxonium ylide: A quantum chemical study

The conversion of methylenedimethyloxonium ylide to ethyl methyl ether was investigated by the semiempirical MNDO method. An activation energy of 51 kJ/mol suggests that this rearrangement is a possible elementary reaction in the well-known MTG process.

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