Equivalent potential of water molecules for electronic structure of glutamic acid

The fundamental importance of the electronic structure of molecules is widely recognized. To get reliable electronic structure of protein in aqueous solution, it is necessary to construct a simple, easy-use equivalent potential of water molecules for protein's electronic structure calculation. Here, the first-principles, all-electron, ab initio calculations have been performed to construct the equivalent potential of water molecules for the electronic structure of glutamic acid, which is a hydrophilic amino acid and is negatively charged (Glu(-)) in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Glu(-) and water molecules is calculated by free cluster calculation. Then, based on the geometric structure, the electronic structure of Glu(-) with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Glu(-) with the potential of dipoles is calculated. Our calculations show that the major effect of water molecules on Glu(-)'s electronic structure is lowering the occupied electronic states by about 0.017 Ry, and broadening energy gap by 12%. The effect of water molecules on the electronic structure of Glu(-) can be well simulated by dipoles potential.     

The equivalent potential of water for electronic structure of aspartic acid

The equivalent potential of water for the electronic structure of aspartic acid (Asp(-)) in solution is constructed by the first-principles, all-electrons, ab initio calculations. Aspartic acid is a hydrophilic amino acid which is negatively charged in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Asp(-) and water molecules is calculated by the free cluster calculation. Then, based on the obtained geometric structure, the electronic structure of Asp(-) with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Asp(-) with the potential of dipoles is calculated. The results show that the major effect of water on Asp(-)'s electronic structure is lowering the occupied molecular orbitals by about 0.02 Ry on average, and narrowing energy gap by 10.8%. The effect of water on the electronic structure of Asp(-) can be simulated by dipoles potential.     

The Suitability of Water Molecule Models for Constructing the Equivalent Potential of Water for the Electronic Structures of Proteins

An equivalent potential of water is needed to calculate the electronic structure of a protein in solution. The previous continuous medium model of water is not suitable. By using dipole, the equivalent potentials of water for the electronic structures of fifteen amino acids have been constructed. In this paper, two water molecule models, the SPC model and TIP4P-FQ models, made up of three point charges, are tested for constructing the equivalent potential of water for the electronic structures of alanine, histidine and serine. At least for these three amino acids, neither the original water molecule model nor the adjusted one is better than the dipole in constructing the equivalent potential of water for the electronic structure of an individual amino acid.     

A Computer Simulation of the Electronic Structure of Leucine in Aqueous Solution

In order to obtain the electronic structure of leucine (Leu) in aqueous solution, we studied three systems: Leu+7H₂O, Leu+8H₂O and Leu+9H₂O. The results indicated that the system Leu+8H₂O was the only choice which was both acceptable and doable: its computational effort was affordable, and it could simulate a main part of the solvent effect on the electronic structure of Leu in solution. Based on the system Leu+8H₂O, all-electron, ab initio calculations were performed to construct an equivalent potential of water for the electronic structure of Leu with dipoles. The results showed that the main effect of water on the electronic structure of Leu was raising the occupied states about 0.0824 Ry on average, and broadening the energy gap by 11%. The water effect on the electronic structure of Leu could be well simulated by the dipole potential. The obtained equivalent potential can be applied directly to the electronic structure calculation of proteins in solution.     

Grid‐based density functional calculations of many‐electron systems

Exploratory variational pseudopotential density functional calculations are performed for the electronic properties of many‐electron systems in the 3D cartesian coordinate grid (CCG). The atom‐centered localized gaussian basis set, electronic density, and the two‐body potentials are set up in the 3D cubic box. The classical Hartree potential is calculated accurately and efficiently through a Fourier convolution technique. As a first step, simple local density functionals of homogeneous electron gas are used for the exchange‐correlation potential, while Hay‐Wadt‐type effective core potentials are employed to eliminate the core electrons. No auxiliary basis set is invoked. Preliminary illustrative calculations on total energies, individual energy components, eigenvalues, potential energy curves, ionization energies, and atomization energies of a set of 12 molecules show excellent agreement with the corresponding reference values of atom‐centered grid as well as the grid‐free calculation. Results for three atoms are also given. Combination of CCG and the convolution procedure used for classical Coulomb potential can provide reasonably accurate and reliable results for many‐electron systems. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

thermocalc — A poor man's approach to computational thermochemistry

We present thermocalc, a Perl module to perform the automated calculation of atomization energies and heats of formation for lists of molecules. The methods used are based on density functional theory and second‐order perturbation theory to ensure that data sets of medium sized to large molecules can be run at reasonable throughput rates. The quantum chemical calculations are performed using the program package TURBOMOLE in a three‐step protocol. In a first step, a pre‐optimization of the structure and a zero‐point energy calculation are performed. As second step, a geometry optimization is being carried out, and the last step is a single point energy calculation. The level of theory used in the different steps can be modified by the user to allow for customized protocols. The performance of example protocols is investigated on different test sets of molecules. In the course of this work, a simple, but efficient one‐parameter correction term based on the shared electron numbers has been developed, which reduces the error of calculated heats of formation significantly. © 2012 Wiley Periodicals, Inc.     

Synthesis,characterization, electronic structure,and non‐linear optical properties (NLO) of Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) complexes with 5‐phenylazo‐8‐hydroxyquinoline using DFT approach

5‐phenylazo‐8‐hydroxyquinoline and its newly metal complexes with Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) metal ions have been prepared and characterized using different analytical techniques. The complexes are distorted octahedral binding via one oxygen and nitrogen atoms of the ligand; two/three coordinated water molecules. 1:1 complexes contain one chloride or OH⁻ ion and some complexes have one or two water of hydration whereas 1:2 complexes contain only two coordinated water molecules in their coordination spheres. All complexes behave as neutral in dimethylformamide (DMF). The electronic structure and non‐linear optical parameters NLO of the complexes (ML and ML2) are investigated theoretically at the B3LYP/GEN level of theory. The geometries of the studied complexes are non‐planner. The calculated E_HOMO and E_LUMO energies of the studied complexes were used to calculate the global properties; hardness (η), global softness (S) and electronegativity (χ). The total dipole moment (μ_tot), static total and anisotropy of polarizability (α, Δα) and static first hyperpolarizability (β) values were calculated and compared with urea as a reference compound. The studied complexes show promising optical properties.     

Design of high‐performance chlorine type dyes for dye‐sensitized solar cells

Intrinsic defect of electronic structure for the chlorine‐type porphyrin 1, which was synthesized for use in dye‐sensitized solar cell (DSSC), is found by theoretical calculation including density functional method (DFT), time‐dependent DFT, and C+/C? function. It is believed that the limited cell performance obtained by using dye 1 as the sensitizer is due to the existence of this electronic defect. To avoid this defect, a series of novel molecules with electron deficient π bridge were designed. The subsequent theoretical calculation indicated that the electron deficient π bridge in the newly designed molecule is quite effective in offsetting the electronic defect observed for dye 1. The parameters for the designed molecules closely associated with open‐circuit voltage and short‐circuit current density including dipole moment of dye vertical to the surface of semiconductor and light‐harvesting efficiency were then evaluated. By comparing these parameters of designed dyes with those of dye 1, we can predict that the DSSC based on dye 4 (2, 6‐cyan benzoic acid as anchoring group) should possess enhanced performance, which would be a valuable theoretical guidance for the practical work. © 2013 Wiley Periodicals, Inc.     

Automated error control in divide‐and‐conquer self‐consistent field calculations

In linear‐scaling divide‐and‐conquer (DC) electronic structure calculations, a buffer region is used to control the error introduced by the DC approximation. In this study, an energy‐based error estimation scheme is proposed for the DC self‐consistent field method with a two‐layer buffer region scheme. Based on this scheme, a procedure to automatically determine the appropriate buffer region in the DC method is proposed. It was confirmed that the present method works satisfactorily in calculations of water clusters and proteins, although its performance was insufficient for the calculation of a delocalized graphene system. © 2018 Wiley Periodicals, Inc.     

An analytic potential energy function for the amide–amide and amide–water intermolecular hydrogen bonds in peptides

An analytic potential energy function is proposed and applied to evaluate the amide–amide and amide–water hydrogen‐bonding interaction energies in peptides. The parameters in the analytic function are derived from fitting to the potential energy curves of 10 hydrogen‐bonded training dimers. The analytic potential energy function is then employed to calculate the N? H…O?C, C? H…O?C, N? H…OH₂, and C?O…HOH hydrogen‐bonding interaction energies in amide–amide and amide–water dimers containing N‐methylacetamide, acetamide, glycine dipeptide, alanine dipeptide, N‐methylformamide, N‐methylpropanamide, N‐ethylacetamide and/or water molecules. The potential energy curves of these systems are therefore obtained, including the equilibrium hydrogen bond distances R(O…H) and the hydrogen‐bonding energies. The function is also applied to calculate the binding energies in models of β‐sheets. The calculation results show that the potential energy curves obtained from the analytic function are in good agreement with those obtained from MP2/6‐31+G** calculations by including the BSSE correction, which demonstrate that the analytic function proposed in this work can be used to predict the hydrogen‐bonding interaction energies in peptides quickly and accurately. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Relativistic, quantum electrodynamic and many-body effects in the water molecule

Ab initio calculations are reported of the electronic structure of the water molecule, based on the Dirac theory of the electron using correlation consistent basis sets. We calculate electron correlation corrections by second-order many-body perturbation theory, NMR shielding constants in the four-component relativistic interaction Hamiltonian formulation of QED, and report the first calculation of the electronic structure of a molecular system in which the Breit interaction is included both perturbatively and variationally in the calculation of the total energy.     

Ab initio properties of Li-group-II molecules for ultracold matter studies

We perform a systematic investigation of the electronic properties of the (2)Σ(+) ground state of Li-alkaline-earth dimers. These molecules are proposed as possible candidates for quantum simulation of lattice-spin models. We apply powerful quantum chemistry coupled-cluster method and large basis sets to calculate potential energies and permanent dipole moments for the LiBe, LiMg, LiCa, LiSr, and LiYb molecules. Agreement of calculated molecular constants with existing experimental data is better than or equal to 8%. Our results reveal a surprising irregularity in the dissociation energy and bond length with an increase in the reduced mass of the molecule. At the same time, the permanent dipole moment at the equilibrium separation has the smallest value between 0.01 a.u. and 0.1 a.u. for the heaviest (LiSr and LiYb) molecules and increases to 1.4 a.u. for the lightest (LiBe), where 1 a.u. is one atomic unit of dipole moment. We consider our study of the (2)Σ(+) molecules a first step towards a comprehensive analysis of their interactions in an optical trap.     

The predicted spectrum of the hypermetallic molecule MgOMg

The present study of MgOMg is a continuation of our theoretical work on Group 2 M(2)O hypermetallic oxides. Previous ab initio calculations have shown that MgOMg has a linear (1)Σ(g)+ ground electronic state and a very low lying first excited triplet electronic state that is also linear; the triplet state has (3)Σ(u)+ symmetry. No gas phase spectrum of this molecule has been assigned, and here we simulate the infrared absorption spectrum for both states. We calculate the three-dimensional potential energy surface, and the electric dipole moment surfaces, of each of the two states using a multireference configuration interaction (MRCISD) approach based on full-valence complete active space self-consistent field (FV-CASSCF) wavefunctions with a cc-pCVQZ basis set. A variational MORBID calculation using our potential energy and dipole moment surfaces is performed to determine rovibrational term values and to simulate the infrared absorption spectrum of the two states. We also calculate the dipole polarizability of both states at their equilibrium geometry in order to assist in the interpretation of future beam deflection experiments. Finally, in order to assist in the analysis of the electronic spectrum, we calculate the vertical excitation energies, and electric dipole transition matrix elements, for six excited singlet states and five excited triplet states using the state-average full valence CASSCF-MRCISD/aug-cc-pCVQZ procedure.     

The influence of electron donor and electron acceptor groups on the electronic structure of the anti‐inflammatory tripeptide Cys‐Asn‐Ser

It has been discussed in the literature that electron delocalization along the peptide backbone and side chain modulates the physical and chemical features of peptides and proteins. The structure and properties of peptides are determined by their charge‐density distribution, such that the modification of its side chain plays an important role on its electronic structure and physicochemical properties. Research on Entamoeba histolytica soluble factors led to the identification of the pentapeptide Met‐Gln‐Cys‐Asn‐Ser, with anti‐inflammatory in vivo and in vitro effects. A synthetic pentapeptide, Met‐Pro‐Cys‐Asn‐Ser, maintained the same anti‐inflammatory actions in experimental assays. A previous theoretical study allowed proposing the Cys‐Asn‐Ser tripeptide (CNS tripeptide) as the pharmacophore group of both molecules. This theoretical hypothesis was recently confirmed experimentally. The objective of this work was to study the influence of the electron donor and electron withdrawing substituent groups on the electronic structure and physicochemical properties of the CNS tripeptide derivatives through a theoretical study at the density functional theory level of theory. Our results in deprotonation energies showed that the relative acidity of hydrogen atom (H2) of the serine‐amide group increases with the electron withdrawing groups. This result was confirmed by means of a study of bond order. The proton affinities illustrated that the electron donor groups favored the basicity of the amino group of the cysteine amino acid. Atomic charges, Frontier molecular orbitals (HOMO–LUMO), and electrostatic potential isosurface and its geometric parameters permitted to analyze the effect that provoked the electron donor and electron attractor groups on its electronic structure and physicochemical features and to identify some reactive sites that could be associated with the anti‐inflammatory activity of tripeptide CNS derivatives. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2398–2410, 2010     

Chemical reaction dynamics of PeCB and TCDD decomposition: A tight‐binding quantum chemical molecular dynamics study with first‐principles parameterization

The decomposition reaction dynamics of 2,3,4,4′,5‐penta‐chlorinated biphenyl (2,3,4,4′,5‐PeCB), 3,3′,4,4′,5‐penta‐chlorinated biphenyl (3,3′,4,4′,5‐PeCB), and 2,3,7,8‐tetra‐chlorinated dibenzo‐p‐dioxin (2,3,7,8‐TCDD) was clarified for the first time at atomic and electronic levels, using our novel tight‐binding quantum chemical molecular dynamics method with first‐principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional first‐principles molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first‐principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4′,5‐PeCB, 3,3′,4,4′,5‐PeCB, and 2,3,7,8‐TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight‐binding quantum chemical molecular dynamics method with first‐principles parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

The investigation on the relative stability of different clusters of thiourea dioxide in water using gas phase quantum chemical calculations

The relative stability of different clusters of thiourea dioxide (TDO) in water is examined using gas phase quantum chemical calculations at the MP2 and B3LYP level with 6‐311++G(d,p) basis set. The possible equilibrium structures and other energetic and geometrical data of the thiourea dioxide clusters, TDO‐(H₂O)_n (n is the number of water molecules), are obtained. The calculation results show that a strong interaction exists between thiourea dioxide and water molecules, as indicated by the binding energies of the TDO clusters progressively increased by adding water molecules. PCM model is used to investigate solvent effect of TDO. We obtained a negative hydration energy of ?20.6 kcal mol^?1 and free‐energy change of ?21.0 kcal mol^?1 in hydration process. On the basis of increasing binding energies with adding water molecules and a negative hydration energy by PCM calculation, we conclude thiourea dioxide can dissolve in water molecules. Furthermore, the increases of the C? S bond distance by the addition of water molecules show that the strength of the C? S bonds is attenuated. We find that when the number of water molecules was up to 5, the C? S bonds of the clusters, TDO‐(H₂O)₅ and TDO‐(H₂O)₆ were ruptured. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Numerical coupled Liouville approach: Application to second hyperpolarizability of molecular aggregate

In our previous study [Int. J. Quant. Chem., to appear], we have developed a novel numerical calculation scheme for a dynamics of quantum network for linear molecular aggregates under intense time‐dependent electric fields. In this approach, each molecule is assumed to be an electric dipole arranged linearly with an angle from the longitudinal axis, and the molecular interactions are taken into account by adding the radiations from these dipoles to the external electric fields. The effects of the radiations from all the dipoles involve the intermolecular distance, the speed of light, retarded polarization, and its first‐ and second‐order time derivatives at the position of each dipole. The quantum dynamics is performed by solving coupled Liouville equations composed of the Liouville equation for each dipole. In the present study, we develop a calculation approach of nonperturbative second hyperpolarizability γ in our novel approach and examine the γ of dimer models composed of two‐state molecules under the one‐photon near resonant intense laser fields. Similar phase transition‐like behavior in the field‐intensity dependence of the γ is observed. We also investigate the second hyperpolarizability spectra in the three‐photon resonant region for dimers composed of three‐state molecules, which mimic the electronic states of allyl cation. Contrary to the one‐photon resonant case, phase transition‐like behavior is not observed in the intensity dependence of γ in the three‐photon resonant region. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 295–306, 1999     

On the choice of a reference state for one‐step perturbation calculations between polar and nonpolar molecules in a polar environment

One‐step perturbation is an efficient method to estimate free energy differences in molecular dynamics (MD) simulations, but its accuracy depends critically on the choice of an appropriate, possibly unphysical, reference state that optimizes the sampling of the physical end states. In particular, the perturbation from a polar moiety to a nonpolar one and vice versa in a polar environment such as water poses a challenge which is of importance when estimating free energy differences that involve entropy changes and the hydrophobic effect. In this work, we systematically study the performance of the one‐step perturbation method in the calculation of the free enthalpy difference between a polar water solute and a nonpolar “water” solute molecule solvated in a box of 999 polar water molecules. Both these polar and nonpolar physical reference states fail to predict the free enthalpy difference as obtained by thermodynamic integration, but the result is worse using the nonpolar physical reference state, because both a properly sized cavity and a favorable orientation of the polar solute in a polar environment are rarely, if ever, sampled in a simulation of the nonpolar solute in such an environment. Use of nonphysical soft‐core reference states helps to sample properly sized cavities, and post‐MD simulation rotational and translational sampling of the solute to be perturbed leads to much improved free enthalpy estimates from one‐step perturbation. © 2012 Wiley Periodicals, Inc.     

Surface Charges at the CaF2/Water Interface Allow Very Fast Intermolecular Vibrational‐Energy Transfer

We investigate the dynamics of water in contact with solid calcium fluoride, where at low pH, localized charges can develop upon fluorite dissolution. We use 2D surface‐specific vibrational spectroscopy to quantify the heterogeneity of the interfacial water (D₂O) molecules and provide information about the sub‐picosecond vibrational‐energy‐relaxation dynamics at the buried solid/liquid interface. We find that strongly H‐bonded OD groups, with a vibrational frequency below 2500 cm^?1, display very rapid spectral diffusion and vibrational relaxation; for weakly H‐bonded OD groups, above 2500 cm^?1, the dynamics slows down substantially. Atomistic simulations based on electronic‐structure theory reveal the molecular origin of energy transport through the local H‐bond network. We conclude that strongly oriented H‐bonded water molecules in the adsorbed layer, whose orientation is pinned by the localized charge defects, can exchange vibrational energy very rapidly due to the strong collective dipole, compensating for a partially missing solvation shell.     

Truxene‐Based Columnar Liquid Crystals: Self‐Assembled Structures and Electro‐Active Properties

Columnar liquid‐crystalline (LC) truxene derivatives containing branched flexible alkyl chains have been designed and synthesized. The dicyanomethylene and dithiafulvene substituents have been introduced into the π‐conjugated truxene framework to tune their electronic and redox properties as well as the molecular assembled structures. The π‐conjugated cores of dicyanomethylene‐ and dithiafulvene‐appended truxenes adopt bowl‐shaped conformations, giving rise to a large intrinsic dipole moment perpendicular to the aromatic framework. These molecules form stable columnar LC structures through intermolecular dipole–dipole interactions. The redox properties of LC truxene derivatives have been examined by cyclic voltammetry. The dicyanomethylene‐appended truxene shows the reversible four‐step electrochemical reductions, whereas the dithiafulvene‐appended truxene undergoes three‐step oxidations.