Time-dependent approach to electronically excited states of molecules with the multiconfiguration time-dependent Hartree-Fock method

In this paper the authors show how the multiconfiguration time-dependent Hartree-Fock (MCTDHF) method can be used for the calculation of electronic properties of molecules associated with the population of excited states. In contrast to other methods for correlated electron dynamics, such as configuration interaction, MCTDHF does not rely on a solution of the electronic Schrodinger equation prior to the propagation. The authors apply this approach to the calculation of vertical excitation energies, transition dipole moments, and oscillator strengths for two test molecules, lithium hydride and methane.     

A non-orthogonal Kohn-Sham method using partially fixed molecular orbitals

A density functional theory method using partially fixed molecular orbitals (PFMOs) is presented. The PFMOs, which have some fixed molecular orbital coefficients and are non-orthogonal, are a generalization of the extreme localized orbitals (ELMOs) of Couty, Bayse, and Hall (1997) Theor Chem Acc 97:96. A non-orthogonal Kohn-Sham method with these PFMOs is derived, and is applied to molecular calculations on the ionization potential of pyridine, the energy difference between cis- and trans-butadiene, the reaction barrier height of the cyclobutene-cis-butadiene interconversion, and the potential energy curve of the hydrogen shift reaction of hydroxycarbene to formaldehyde. The PFMO Kohn-Sham method reproduces well the results of the full Kohn-Sham method without having a restriction on the molecular orbital coefficients. The difference is less than 0.1 eV in the ionization potential and about 0.1 kcal/mol in the barrier height and in the potential energy calculations.     

Mixing of generalized parity in molecular orbitals

The concept of generalized parity is introduced. It allows mixing of different symmetries in molecular orbitals in the framework of the Parity Mixing in Orbitals method. An extension of this SCF calculational scheme is also discussed and the relevant secular equations are reported.Alexander von Humboldt Fellow. On leave from the Institute Rudjer Bokovi, Zagreb, Croatia, Yugoslavia.     

Molecular dynamics method in studies of molecular film growth processes

This review is an attempt to analyze some of the experimental problems arising in the course of growth of orientated molecular films using metal monophthalocyanine (MPc) films as an example and to demonstrate the possibilities of molecular dynamics simulation of these processes for solving experimental problems. Examples of theoretical simulation of adsorption processes are given; formation of a molecular monolayer is considered for copper phthalocyanine films as an example.     

The generalized molecular fractionation with conjugate caps/molecular mechanics method for direct calculation of protein energy

A generalized molecular fractionation with conjugate caps/molecular mechanics (GMFCC/MM) scheme is developed for efficient linear-scaling quantum mechanical calculation of protein energy. In this GMFCC/MM scheme, the interaction energy between neighboring residues as well as between non-neighboring residues that are spatially in close contact are computed by quantum mechanics while the rest of the interaction energy is computed by molecular mechanics. Numerical studies are carried out to calculate torsional energies of six polypeptides using the GMFCC/MM approach and the energies are shown to be in general good agreement with the full system quantum calculation. Among those we tested is a polypeptide containing 396 atoms whose energies are computed at the MP26-31G* level. Our study shows that using GMFCC/MM, it is possible to perform high level ab initio calculation such as MP2 for applications such as structural optimization of protein complex and molecular dynamics simulation.     

Quantum dynamics of dissociative adsorption of H_2 and D_2:The time-dependent wave packet method

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Molecular Structure and Dynamics of Water at the Water–Air Interface Studied with Surface‐Specific Vibrational Spectroscopy

Water interfaces provide the platform for many important biological, chemical, and physical processes. The water–air interface is the most common and simple aqueous interface and serves as a model system for water at a hydrophobic surface. Unveiling the microscopic (<1 nm) structure and dynamics of interfacial water at the water–vapor interface is essential for understanding the processes occurring on the water surface. At the water interface the network of very strong intermolecular interactions, hydrogen‐bonds, is interrupted and the density of water is reduced. A central question regarding water at interfaces is the extent to which the structure and dynamics of water molecules are influenced by the interruption of the hydrogen‐bonded network and thus differ from those of bulk water. Herein, we discuss recent advances in the study of interfacial water at the water–air interface using laser‐based surface‐specific vibrational spectroscopy.     

Quantum mechanical/molecular mechanical self-consistent Madelung potential method for treatment of polar molecular crystals

The self-consistent Madelung potential (SCMP) approach for calculating molecular wave functions for a subunit embedded in a symmetrical environment constituted by the copies of the subunit is implemented with semiempirical NDDO model Hamiltonians and supplemented with empirically parameterized dispersion–repulsion interaction potentials. This model yields sublimation enthalpies in good agreement with available experimental data for a series of molecular crystals, including imidazol, benzimidazole, urea, urethane, dicyaneamide, formamide, uracil, cytosine, maleic anhydride, succinic anhydride, and 1,3,5-triamino-2,4,6-trinitro-benzene. The SCMP-NDDO method, which avoids difficulties concerning the parametrization of charges in the molecular mechanics force fields, is proposed mainly for the treatment of molecular crystals with large unit cells. It might be particularly useful where important charge reorganization is expected under the effect of the crystal field. Charge distributions, obtained by the SCMP and the simple dielectric cavity self-consistent reaction field models, are compared and analyzed. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 38–50, 1998     

Fourier transform Raman and DFT study of three annulated oligothiophenes with different molecular shapes.

Herein, we study the conjugation properties of three different thienoacenes, each of which has three or four fused thiophene rings, by means of Fourier transform Raman spectroscopy. The B3LYP/6-31G** vibrational analysis of all of the collected spectroscopic data evidences that the selective enhancement of a limited number of Raman scatterings is related to the occurrence in the three thienoacenes of a vibronic coupling between the lowest unoccupied frontier molecular orbital (LUMO) and some Raman-active skeletal nu(C==C) stretching modes of 1600-1300 cm(-1).     

Calculations of molecular polarizabilities using the Valence Effective Hamiltonian (VEH) method

In this paper, we investigate the applicability of the Valence Effective Hamiltonian (VEH) method to calculations of theoretical molecular linear polarizabilities by the Sum-Over-States (SOS) methodology. Test calculations are presented on the polyene series. They indicate that the method gives qualitatively the same trends asab initio small basis sets calculations.Dedicated to Professor J. Koutecký on the occasion of his 65th birthday     

光谱-分子模拟法分析杨梅素与人血清白蛋白的分子作用机制

在模拟生理条件下,用多种光谱法结合分子对接法测定了杨梅素(MY)与人血清白蛋白(HSA)的相互作用.研究结果表明,MY能够明显猝灭HSA的荧光,MY与HSA的相互作用为复合式静态结合过程,结合强度较强.热力学和分子对接结果表明,MY与HSA是自发结合的,维持MY与HSA的相互作用力主要是氢键和范德华力.能量转移结果表明...     

Exploring meso-/microporous composite molecular sieves with core-shell structures

A series of core–shell‐structured composite molecular sieves comprising zeolite single crystals (i.e., ZSM‐5) as a core and ordered mesoporous silica as a shell were synthesized by means of a surfactant‐directed sol–gel process in basic medium by using cetyltrimethylammonium bromide (CTAB) as a template and tetraethylorthosilicate (TEOS) as silica precursor. Through this coating method, uniform mesoporous silica shells closely grow around the anisotropic zeolite single crystals, the shell thickness of which can easily be tuned in the range of 15–100 nm by changing the ratio of TEOS/zeolite. The obtained composite molecular sieves have compact meso‐/micropore junctions that form a hierarchical pore structure from ordered mesopore channels (2.4–3.0 nm in diameter) to zeolite micropores (≈0.51 nm). The short‐time kinetic diffusion efficiency of benzene molecules within pristine ZSM‐5 (≈7.88×10^?19 m² s^?1) is almost retainable after covering with 75 nm‐thick mesoporous silica shells (≈7.25×10^?19 m² s^?1), which reflects the greatly opened junctions between closely connected mesopores (shell) and micropores (core). The core–shell composite shows greatly enhanced adsorption capacity (≈1.35 mmol g^?1) for large molecules such as 1,3,5‐triisopropylbenzene relative to that of pristine ZSM‐5 (≈0.4 mmol g^?1) owing to the mesoporous silica shells. When Al species are introduced during the coating process, the core–shell composite molecular sieves demonstrate a graded acidity distribution from weak acidity of mesopores (predominant Lewis acid sites) to accessible strong acidity of zeolite cores (Lewis and Brønsted acid sites). The probe catalytic cracking reaction of n‐dodecane shows the superiority of the unique core–shell structure over pristine ZSM‐5. Insight into the core–shell composite structure with hierarchical pore and graded acidity distribution show great potential for petroleum catalytic processes.     

Evaluation of molecular integral of Cartesian Gaussian type basis function with complex‐valued center coordinates and exponent via the McMurchie–Davidson recursion formula,and its application to electron dynamics

McMurchie–Davidson recursion formula is extended to derive the ab initio molecular integrals with higher angular quantum number complex Gaussian type basis function which has complex‐valued center coordinates and a complex‐valued exponent. Using the analytical recursion formulae, some calculations of electronic dynamics after beta decay of tritium hydride molecular ion HT⁺ are performed by a quantum wave packet method with thawed Gaussian basis functions of s‐ and p‐type. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Synthesis and supramolecular properties of molecular clips with anthracene sidewalls

Novel molecular clips with anthracene sidewalls (1 a-c) were synthesized; they form stable host-guest complexes with a variety of electron-deficient aromatic and quinoid molecules. According to single-crystal structure analyses of clip 1 c and 1,2,4,5-tetracyanobenzene (TCNB) complex 14@1 b, the clips' anthracene sidewalls have to be compressed substantially during the complex formation to provide attractive pi-pi interactions between the aromatic guest molecule and the two anthracene sidewalls in the complex. The compression and expansion of aromatic sidewalls are calculated by molecular mechanics to be low-energy processes, so the energy required for compression of the anthracene sidewalls during complex formation is apparently overcompensated by the gain in energy resulting from the attractive pi-pi interactions. The finding that complexes of the clips 1 a-c are more stable than those of the corresponding clips 2 a-c can be explained in terms of the larger van der Waals contact surfaces of the anthracene sidewalls in 1 a-c (relative to the naphthalene sidewalls in 2 a-c). Color changes resulting from charge-transfer (CT) bands are observed in complex formation by 1 a-c: from colorless to red or purple with TCNB (14), and from yellow to green with 2,4,7-trinitro-9-fluorenone TNF (17). Independently, the host 1 b and guest 14 fluoresce from their respective excited singlet states, whilst in the complex 14@1 b the charge-transfer state quenches the higher-energy singlet states of the two components, and as a result luminescence is only observed from this new CT state. To the best of our knowledge, complex 14@1 b is the first example of CT luminescence from a host-guest complex. The binding constant determined for the formation of the TCNB complex 14@1 b from a UV/Vis titration experiment (Ka = 12 400 m(-1)) agrees well with the value (K(a) = 12 800 m(-1)) obtained by 1H NMR titration.     

Study of molecular structures for arylidene derivatives of 3R‐methylcyclohexanone by 1H NMR and molecular simulation

Conformational states of the cyclohexanone ring were established for 3R‐methyl‐6‐(4‐phenylbenzylidene)cyclohexanone and several 2,6‐bis(4‐X‐benzylidene)‐3R‐methylcyclohexanones (X = Br, OCOCH₃ and C₆H₅) by ¹H NMR spectroscopy combined with molecular simulation using the semi‐empirical methods AM1 and PM3. The first compound studied contains only one arylidene group, and exists predominantly in a chair conformation of the cyclohexanone ring with an equatorial orientation of the methyl substituent in C₆D₆ and CDCl₃ solutions at room temperature (22–23 °C). In contrast, the 2,6‐bis(arylidene) derivatives of 3R‐methylcyclohexanone preferentially adopt conformations with an axially oriented methyl group. The extent of twisting of enone fragments was also characterized for the compounds studied based on simulation results and comparison of chemical shifts for the arylidene protons of appropriate model compounds. Copyright © 2003 John Wiley & Sons, Ltd.     

Facile optical resolution of tert-butanethiosulfinate by molecular complexation with (R)-BINOL and study of chiral discrimination of the diastereomeric complexes

An important synthon, tert-butanethiosulfinate (2), has been effectively resolved by forming molecular complexes with (R)-2,2'-dihydroxy-1,1'-binaphthyl (BINOL, 3) in high enantioselectivity (>99 % ee). The present procedure represents the first example of the resolution of thiosulfinate. The mechanism of chiral discrimination is discussed in terms of molecular recognition based on IR and Xray analyses of the diastereomeric complexes during the resolution. In the less-soluble complex, (R)-3 and (R)-2 self-assembled as a linear supramolecule; however, in the more-soluble complex, (R)-3 and (S)-2 formed a simple bimolecular complex by one stronger hydrogen bond. Hydrogen bonding is the major driving force for effective resolution.     

Redox-controlled interaction of biferrocenyl-terminated dendrimers with beta-cyclodextrin molecular printboards

This paper describes the synthesis and electrochemistry of biferrocenyl-terminated dendrimers and their beta-cyclodextrin (beta-CD) inclusion complexes in aqueous solution and at surfaces. Three generations of poly(propylene imine) (PPI) dendrimers, decorated with 4, 8, and 16 biferrocenyl (BFc) units, respectively, were synthesized. A water-soluble BFc derivative forms stable inclusion complexes with beta-CD. The intrinsic binding constant is K(i)=2.5 x 10(4) M(-1). The BFc dendrimers were solubilized in water by complexation of the end groups with beta-CD, resulting in large water-soluble supramolecular assemblies. Cyclic voltammetry (CV) and differential pulse voltammetry (DPV) showed that all the end groups are complexed to beta-CD. Adsorption of the dendrimers at self-assembled monolayers (SAMs) of heptathioether-functionalized beta-CD on gold ("molecular printboards") resulted in stable monolayers of the dendrimers due to the formation of multivalent host-guest interactions between the BFc end groups of the dendrimers and the immobilized beta-CD molecules. The number of interacting end groups is 3, 4, and 4 for dendrimer generations 1, 2, and 3, respectively. The complexation of BFc to beta-CD is sensitive to the oxidation state of the BFc unit. Oxidation of neutral BFc-Fe(2) ((II,II)) to the cationic, mixed-valence biferrocenium BFc-Fe(2) ((II,III)+) resulted in dissociation of the host-guest complexes. Scan-rate-dependent CV and DPV analyses of the dendrimer-beta-CD assemblies immobilized at the beta-CD host surface and in solution revealed that the dendrimers are oxidized in three steps. First, the surface-beta-CD-bound BFc moieties are oxidized to the mixed-valence state, Fe(2) ((II,III)+), followed by the oxidation of the non-surface-interacting BFc groups to the Fe(2) ((II,III)+) state. The third step involves the oxidation of all the BFc moieties to the Fe(2) ((III,III)2+) state.